Histone deacetylase inhibitors

ABSTRACT

The compounds provided herein are phenyl analine amides and are useful for inhibiting histone deacteylase (“HDAC”) enzymes, such as HDAC1, HDAC2, and HDAC3.

TECHNICAL FIELD

This invention relates to generally inhibiting histone deacetylase(“HDAC”) enzymes (e.g., HDAC1, HDAC2, and HDAC3).

BACKGROUND

To date, 18 HDACs have been identified in humans and there is increasingevidence that the 18 histone deacetylases (HDAC) in humans are notredundant in function. HDACs are classified into three main groups basedon their homology to yeast proteins. Class I includes HDAC1, HDAC2,HDAC3, and HDAC8 and have homology to yeast RPD3. HDAC4, HDAC5, HDAC7,and HDAC9 belong to class IIa and have homology to yeast HDAC1. HDAC6and HDAC10 contain two catalytic sites and are classified as class IIb,whereas HDAC11 has conserved residues in its catalytic center that areshared by both class I and class II deacetylases and is placed in classIV. These HDACs contain zinc in their catalytic site and are inhibitedby compounds like trichostatin A (TSA) and vorinostat [suberoylanilidehydroxamic acid (SAHA)]. Class III HDACs are known as sirtuins. Theyhave homology to yeast Sir2, require NAD⁺ as cofactor, and do notcontain zinc in the catalytic site. In general, HDAC inhibitors ofzinc-dependent HDACs include a Zn-binding group, as well as a surfacerecognition domain.

HDACs are involved in the regulation of a number of cellular processes.Histone acetyltransferases (HATs) and HDACs acetylate and deacetylatelysine residues on the N termini of histone proteins thereby affectingtranscriptional activity. They have also been shown to regulatepost-translational acetylation of at least 50 non-histone proteins suchas α-tubulin (see for example Kahn, N et al Biochem J 409 (2008) 581,Dokmanovic, M et al Mol Cancer Res 5 (2007) 981).

Altering gene expression through chromatin modification can beaccomplished by inhibiting histone deacetylase (HDAC) enzymes. There isevidence that histone acetylation and deacetylation are mechanisms bywhich transcriptional regulation in a cell—a major event in celldifferentiation, proliferation, and apoptosis—is achieved. It has beenhypothesized that these effects occur through changes in the structureof chromatin by altering the affinity of histone proteins for coiled DNAin the nucleosome. Hypoacetylation of histone proteins is believed toincrease the interaction of the histone with the DNA phosphate backbone.Tighter binding between the histone protein and DNA can render the DNAinaccessible to transcriptional regulatory elements and machinery. HDACshave been shown to catalyze the removal of acetyl groups from theε-amino groups of lysine residues present within the N-terminalextension of core histones, thereby leading to hypoacetylation of thehistones and blocking of the transcriptional machinery and regulatoryelements.

Inhibition of HDAC, therefore can lead to histone deacetylase-mediatedtranscriptional derepression of tumor suppressor genes. For example,cells treated in culture with HDAC inhibitors have shown a consistentinduction of the kinase inhibitor p21, which plays an important role incell cycle arrest. HDAC inhibitors are thought to increase the rate oftranscription of p21 by propagating the hyperacetylated state ofhistones in the region of the p21 gene, thereby making the geneaccessible to transcriptional machinery. Further, non-histone proteinsinvolved in the regulation of cell death and cell-cycle also undergolysine acetylation and deacetylation by HDACs and histone acetyltransferase (HATs).

This evidence supports the use of HDAC inhibitors in treating varioustypes of cancers. For example, vorinostat (suberoylanilide hydroxamicacid (SAHA)) has been approved by the FDA to treat cutaneous T-celllymphoma and is being investigated for the treatment of solid andhematological tumors. Further, other HDAC inhibitors are in developmentfor the treatment of acute myelogenous leukemia, Hodgkin's disease,myelodysplastic syndromes and solid tumor cancers.

HDAC inhibitors have also been shown to inhibit pro-inflammatorycytokines, such as those involved in autoimmune and inflammatorydisorders (e.g. TNF-α). For example, the HDAC inhibitor MS275 was shownto slow disease progression and joint destruction in collagen-inducedarthritis in rat and mouse models. Other HDAC inhibitors have been shownto have efficacy in treating or ameliorating inflammatory disorders orconditions in in vivo models or tests for disorders such as Crohn'sdisease, colitis, and airway inflammation and hyper-responsiveness. HDACinhibitors have also been shown to ameliorate spinal cord inflammation,demyelination, and neuronal and axonal loss in experimental autoimmuneencephalomyelitis (see for example Wanf L et al, Nat Rev Drug Disc 8(2009) 969).

Triplet repeat expansion in genomic DNA is associated with manyneurological conditions (e.g., neurodegenerative and neuromusculardiseases) including myotonic dystrophy, spinal muscular atrophy, fragileX syndrome, Huntington's disease, spinocerebellar ataxias, amyotrophiclateral sclerosis, Kennedy's disease, spinal and bulbar muscularatrophy, Friedreich's ataxia and Alzheimer's disease. Triplet repeatexpansion may cause disease by altering gene expression. For example, inHuntington's disease, spinocerebellar ataxias, fragile X syndrome, andmyotonic dystrophy, expanded repeats lead to gene silencing. InFriedreich's ataxia, the DNA abnormality found in 98% of FRDA patientsis an unstable hyper-expansion of a GAA triplet repeat in the firstintron of the frataxin gene (see Campuzano et al., Science 271:1423(1996)), which leads to frataxin insufficiency resulting in aprogressive spinocerebellar neurodegeneration. Since they can affecttranscription and potentially correct transcriptional dysregulation,HDAC inhibitors have been tested and have been shown to positivelyaffect neurodegenerative diseases (see Herman D et al, Nat Chem Bio 2551(2006) for Friedreich's ataxia, Thomas E A et al, Proc Natl Acad SciUSA 105 15564 (2008) for Huntington's disease).

HDAC inhibitors may also play a role in cognition-related conditions anddiseases. It has indeed become increasingly evident that transcriptionis likely a key element for long-term memory processes (Alberini C M,Physiol Rev 89 121 (2009)) thus highlighting another role forCNS-penetrant HDAC inhibitors. Although studies have shown thattreatment with non-specific HDAC inhibitors such as sodium butyrate canlead to long-term memory formation (Stefanko D P et al, Proc Natl AcadSci USA 106 9447 (2009)), little is known about the role of specificisoforms. A limited number of studies have shown that, within class IHDACs, main target of sodium butyrate, the prototypical inhibitor usedin cognition studies, HDAC2 (Guan J-S et al, Nature 459 55 (2009)) andHDAC3 (McQuown S C et al, J Neurosci 31 764 (2011)) have been shown toregulate memory processes and as such are interesting targets for memoryenhancement or extinction in memory-affecting conditions such as, butnot limited to, Alzheimer's disease, post-traumatic stress disorder ordrug addiction.

HDAC inhibitors may also be useful to treat infectious disease such asviral infections. For example, treatment of HIV infected cells with HDACinhibitors and anti-retroviral drugs can eradicate virus from treatedcells (Blazkova j et al J Infect Dis. 2012 Sep. 1; 206(5):765-9; ArchinN M et al Nature 2012 Jul. 25, 487(7408):482-5).

SUMMARY

In one aspect, a compound of the formula (I) is featured:

-   -   wherein n=0 or 1;    -   I. when n=1, Z is R₁—X—Ar/Het wherein:    -   Ar/Het is:    -   (i) a 5 membered heteroaryl selected from the group consisting        of pyrazolyl, thiazolyl, oxazolyl, imidazolyl, thienyl, furanyl,        isoxazolyl, isothiazolyl, thiadiazolyl, oxadiazolyl, and        1,2,4-triazolyl (in some embodiments, the definition of Ar/Het        can further include 3,5-dimethylpyrazolyl); or    -   (ii) a bicyclic 8-, 9-, or 10-membered heteroaryl selected from        the group consisting of benzofuranyl, benzothienyl,        benzothiazolyl, indolyl, indazolyl, quinolonyl, naphtyridinyl,        indolizinyl, pyrrolopyrimidinyl, pyrazolopyridinyl,        imidazopyridinyl, imidazopyridazinyl, triazolopyridinyl,        imidazothiazolyl, imidazooxazolyl, triazolothiazolyl, and        triazolooxazolyl;    -   X is:    -   (i) —Y—[C(R^(a))₂]_(a)-A-[C(R^(b))₂]_(b)—B—;    -   wherein:    -   Y is bond, CR^(c)═CR^(d), O, NR^(c), or S(O)_(m);    -   each of A and B is, independently, a bond, O, NR^(f), or        S(O)_(m);    -   a is 1-3 (e.g., 1 or 2, e.g., 1);    -   b is 0-3 (e.g., 0, or other than 0, e.g., 1; or 2 or 3);    -   m is 0-2;        -   each occurrence of R^(a) and R^(b) is independently selected            from H, F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂,            OCO—(C1-C6 alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy,            C1-C6 fluoroalkoxy, and cyano; or        -   one or more of the following can apply with respect to R^(a)            and R^(b):        -   any two R^(a), together with the carbons to which each is            attached, together form C3-C6 cycloalkyl or heterocyclyl            including 3-6 ring atoms, in which one of the heterocyclyl            ring atoms is selected from O; S(O)m and NR^(g); in these            embodiments, any remaining occurrences of R^(a) and any            occurrence of R^(b) are each independently defined according            to any one or more of the preceding or following definitions            pertaining to R^(a) and R^(b); or        -   one R^(a) and one R^(b), together with the carbons to which            each is attached, form C3-C6 cycloalkyl or heterocyclyl            including 3-6 ring atoms, in which one of the heterocyclyl            ring atoms is selected from O; S(O)m and NR^(g); in these            embodiments, the other R^(a), the other R^(b), and any other            remaining occurrences of R^(a) and R^(b) are each            independently defined according to any one or more of the            preceding or following definitions pertaining to R^(a) and            R^(b); or        -   any two R^(b), together with the carbons to which each is            attached, form C3-C6 cycloalkyl or heterocyclyl including            3-6 ring atoms, in which one of the ring atoms is selected            from O; S(O)m and NR^(g); in these embodiments, each            occurrence of R^(a) and any other remaining occurrences of            R^(b) are each independently defined according to any one or            more of the preceding or following definitions pertaining to            R^(a) and R^(b);        -   each of R^(c) and R^(d) is, independently, selected from H,            F, OH, C1-C6 alkyl, C3-C5 cycloalkyl, NH₂, OCO—(C1-C6            alkyl), OCO—(C3-C5 cycloalkyl), C1-C6 alkoxy, C1-C6            fluoroalkoxy, and cyano;        -   or R^(c) and R^(d), together with the carbons to which each            is attached form a C5-C7 cycloalkyl or heterocyclyl            including 3-6 ring atoms, in which from 1-2 of the            heterocyclyl ring atoms is/are independently selected from            O; S(O), and NR^(g′);        -   each occurrence of R^(e), R^(f), R^(g) and R^(g′) is            independently selected from H, C1-C6 alkyl, —C(═O)H,            —C(═O)R^(h), C(═O)O(C1-C6 alkyl), C(═O)N(R^(i))₂, SO₂—R^(h),            wherein R^(h) is selected from C1-C6 alkyl, CH₂-(heteroaryl            including 5-10 ring atoms), CH₂—(C6-C10 aryl), and C6-C10            aryl; and each occurrence of R^(i) is independently selected            from H, C1-C6 alkyl, CH₂-(heteroaryl including 5-10 ring            atoms), CH₂—(C6-C10 aryl), and C6-C10 aryl (in embodiments,            the aryl and heteroaryl portion in R^(h) and R^(i) can be            optionally substituted, e.g., with one or more independently            selected substituents such as F, C1-C6 alkyl, fluoro C1-C6            alkyl, C3-C6 cycloalkyl, C1-C6 alkoxy, C1-C6 fluoroalkoxy,            or cyano);    -   further wherein:    -   (a) when each of A and B is a bond, and b is 0, then X has the        following formula: —Y[—C(R^(a))₂]_(a)—;    -   (b) when b is 0 or 1 (e.g., 0), then A and B cannot both be        heteroatoms (i.e., as defined in O, NR^(e), or S(O)_(m)); and    -   (c) when A or B serves as the point of connection of X to        Ar/Het, and the Ar/Het is linked to X via a nitrogen ring atom        in Ar/Het, then the A or B connector cannot be a heteroatom        (i.e., as defined in O, NR^(e), or S(O)_(m));    -   or X is:    -   (ii) direct bond; or    -   (iii) C═O, C(R^(j))₂—C(═O), or C(═O)—C(R^(j))₂, SO₂—NR^(k),        NR^(k)—SO₂, C(═O)NR^(k) and NR^(k)—C(═O); wherein:        -   each occurrence of R^(j) is independently selected from H,            F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6            alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy, C1-C6            fluoroalkoxy, and cyano;        -   or R^(j)—C—R^(j) together form C3-C6 cycloalkyl or            heterocyclyl including 3-6 ring atoms, in which one of the            heterocyclyl ring atoms is selected from O; S(O)m and            NR^(j′);        -   each occurrence of R^(j′) and R^(k) is independently            selected from H, C1-C6 alkyl, —C(═O)H, —C(═O)R^(m),            C(═O)O(C1-C6 alkyl), C(═O)N(R^(n))₂, and SO₂—R^(m), wherein            R^(m) is selected from C1-C6 alkyl, CH₂-heteroaryl,            CH₂-aryl, and aryl; and each occurrence of R^(n) is            independently selected from H, C1-C6 alkyl, CH₂-(heteroaryl            including 5-10 ring atoms), CH₂—(C6-C10 aryl), and C6-C10            aryl (in embodiments, the aryl and heteroaryl portion in            R^(m) and R^(n) can be optionally substituted, e.g., with            one or more independently selected substituents such as F,            C1-C6 alkyl, fluoro C1-C6 alkyl, C3-C6 cycloalkyl, C1-C6            alkoxy, C1-C6 fluoroalkoxy, or cyano);    -   each of R4 and R5 is, independently, selected from H, C1-C6        alkyl and F;    -   R1 is:    -   (i) hydrogen; or    -   (ii) C6-C10 aryl, which is optionally substituted with from 1-3        R^(o); or    -   (iii) monocyclic or bicyclic heteroaryl including from 5-10 ring        atoms, which is optionally substituted with from 1-3 R^(o);        wherein from 1-4 of the ring atoms is/are a heteroatom        independently selected from O, N, N—H, N—R^(o), and S; or    -   (iv) heterocyclyl including from 4-10 ring atoms, which is        optionally substituted with from 1-3 R^(o); wherein from 1-4 of        the ring atoms is/are a heteroatom independently selected from        O, N, N—H, N—R^(o), and S;    -   (in some embodiments, R1 is other than H); and    -   each occurrence of R^(o) is independently selected from the        group consisting of (beginning with halogen and through and        including nitro below):        -   halogen;        -   C1-C6 alkyl; fluoro(C1-C6)alkyl;        -   hydroxyl;        -   hydroxy(C₁-C₄)alkyl;        -   C1-C6 alkoxy; fluoro(C1-C6)alkoxy;        -   (C1-C6 alkyl)C(O)—;        -   (C1-C6 alkyl)NH—; (C1-C6 alkyl)₂N— (which includes, e.g.,            —NMe₂, —NMe(iPr));        -   —N*(R^(o′))₂, wherein R^(o)′—N*—R^(o)′ together form a            saturated ring having 5 or 6 ring atoms, in which 1 or 2            ring atoms (i.e., 1 or 2 ring atoms in addition to the N*            ring atom) is/are optionally a heteroatom independently            selected from NH, N(alkyl), O, or S (—N*(R^(o′))₂ includes            cyclic amino such as, e.g., pyrrolidinyl and morpholinyl);        -   formyl; formyl(C₁-C₄) alkyl; cyano; cyano(C₁-C₄) alkyl;        -   benzyl; benzyloxy;        -   heterocyclyl)-(C0-C6, e.g., C1-C6) alkyl, wherein the            heterocyclyl portion includes 5 or 6 ring atoms, in which 1            or 2 of the ring atoms is/are a heteroatom independently            selected from NH, N(alkyl), O, or S, and when said alkyl            portion is present (i.e., C1-C6), said alkyl portion serves            as the point of attachment to R1 (i.e., the            (heterocyclyl)-(C1-C6) alkyl is connected to R1 via the            alkyl portion); otherwise in the case of C0 alkyl (i.e., no            alkyl portion is present), a heterocyclyl carbon ring atom            serves as the point of attachment of the heterocyclyl to R1;        -   phenyl or heteroaryl including from 5-6 ring atoms, wherein            from 1-4 of the ring atoms is/are a heteroatom independently            selected from O, N, N—H, N−R^(o″), and S, each of which is            optionally substituted with from 1-3 R^(o″);        -   SO₂—(C1-C6)alkyl; SO—(C1-C6)alkyl; and        -   nitro;        -   in embodiments, R^(o) can be any one (or more) of the            substituents listed above and/or R^(o) can be any one or            more of the subsets of substituents listed above (such as            those bulleted above); e.g., R^(o) can be any one (or more)            of the substituents that are present, and/or any one (or            more) of the substituents that encompass those that are            present, in the compounds described herein;    -   each occurrence of R^(o″) is independently selected from the        group consisting of (beginning with halogen and through and        including nitro below):        -   halogen;        -   C1-C6 alkyl; fluoro(C1-C6)alkyl;        -   hydroxyl;        -   hydroxy(C₁-C₄)alkyl;        -   C1-C6 alkoxy; fluoro(C1-C6)alkoxy;        -   (C1-C6 alkyl)C(O)—;        -   (C1-C6 alkyl)NH—; (C1-C6 alkyl)₂N— (which includes, e.g.,            —NMe2, —NMe(iPr));        -   -formyl; formyl(C₁-C₄) alkyl; cyano; cyano(C₁-C₄) alkyl;        -   benzyl; benzyloxy;        -   heterocyclyl)-(C0-C6, e.g., C1-C6) alkyl, wherein the            heterocyclyl portion includes 5 or 6 ring atoms, in which 1            or 2 of the ring atoms is/are a heteroatom independently            selected from NH, N(alkyl), O, or S, and when said alkyl            portion is present (i.e., C1-C6), said alkyl portion serves            as the point of attachment to R1 (i.e., the            (heterocyclyl)-(C1-C6) alkyl is connected to R1 via the            alkyl portion); otherwise in the case of C0 alkyl (i.e., no            alkyl portion is present), a heterocyclyl carbon ring atom            serves as the point of attachment of the heterocyclyl to R1;        -   phenyl or heteroaryl including from 5-6 ring atoms, wherein            from 1-4 of the ring atoms is/are a heteroatom independently            selected from O, N, N—H, N—(C1-C6 alkyl), and S;            SO₂—(C1-C6)alkyl; SO—(C1-C6)alkyl; and nitro;        -   in embodiments, R^(o″) can be any one (or more) of the            substituents listed above and/or R^(o″) can be any one or            more of the subsets of substituents listed above (such as            those bulleted above); e.g., R^(o″) can be any one (or more)            of the substituents that are present, and/or any one (or            more) of the substituents that encompass those that are            present, in the compounds described herein;    -   II. when n=0, Z is R₁—V-Cy-U—Ar′/Het′ wherein:    -   Ar′/Het′ is:        -   (i) phenyl, pyridyl, or pyrimidinyl, each of which is            optionally substituted with from 1-3 R^(p); provided that            the point of connection on said phenyl, pyridyl, or            pyrimidinyl to U (i.e., the connection U—Ar′/Het′ in            formula I) and the point of connection on said phenyl,            pyridyl, or pyrimidinyl to the amide carbonyl (i.e., the            connection Ar′/Het′-C(═O) in formula I) do not result in            1,2-relation to one another on said phenyl, pyridyl, or            pyrimidinyl (i.e., the points of connection to U and C(O) on            said phenyl, pyridyl, or pyrimidinyl are not ortho with            respect to one another); wherein R^(p) at each occurrence            is, independently, selected from H, F, chloro, CH₃, CF₃,            OCH₃, OCF₃, and OCHF₂; or        -   (ii) a 5-membered heteroaryl selected from pyrazolyl,            pyrrolyl, thiazolyl, thienyl, furanyl, imidazolyl, oxazolyl,            oxadiazolyl, thiadiazolyl, isoxazolyl, isothiazolyl, each of            which is optionally substituted with from 1-3 R^(p);            provided that the point of connection on said 5-membered            heteroaryls to U (i.e., the connection U—Ar′/Het′ in            formula I) and the point of connection on said 5-membered            heteroaryls to the amide carbonyl (i.e., the connection            Ar′/Het′-C(═O) in formula I) do not result in 1,2-relation            to one another on said 5-membered heteroaryls (i.e., the            points of connection to U and C(O) on said 5-membered            heteroaryl are not adjacent to one another); or        -   (iii) a 8-, 9- or 10-membered bicyclic heteroaryl selected            from benzothienyl, benzofuranyl, benzothioazolyl,            benzoxazolyl, indolyl, isoindolonyl, indolizinyl,            pyrrolopyrimidinyl, pyrazolopyridinyl, imidazopyridinyl,            imidazopyridazinyl, triazolopyridinyl, imidazothiazolyl,            imidazooxazolyl, quinolinyl, and naphthyridinyl; each of            which is optionally substituted with from 1-3 R^(p);        -   (in some embodiments, Ar′/Het′ is other than a 8-, 9- or            10-membered bicyclic heteroaryl selected from benzothienyl,            benzofuranyl, benzothioazolyl, benzoxazolyl, indolyl,            isoindolonyl, indolizinyl, pyrrolopyrimidinyl,            pyrazolopyridinyl, imidazopyridinyl, imidazopyridazinyl,            triazolopyridinyl, imidazothiazolyl, imidazooxazolyl,            quinolinyl, and naphthyridinyl; each of which is optionally            substituted with from 1-3 R^(p));    -   R1 is:    -   (i) hydrogen; or    -   (ii) C6-C10 aryl, which is optionally substituted with from 1-3        R^(q); or    -   (iii) monocyclic or bicyclic heteroaryl including from 5-10 ring        atoms, which is optionally substituted with from 1-3 R^(q);        wherein from 1-4 of the ring atoms is/are a heteroatom        independently selected from O, N, N—H, N—R^(q), and S; or    -   (iv) heterocyclyl including from 4-10 ring atoms, which is        optionally substituted with from 1-3 R^(q); wherein from 1-4 of        the ring atoms is/are a heteroatom independently selected from        O, N, N—H, N—R^(q), and S; and    -   each occurrence of R^(q) is independently selected from the        group consisting of (beginning with halogen and through and        including nitro below):        -   halogen;        -   C1-C6 alkyl; fluoro(C1-C6)alkyl;        -   hydroxyl;        -   hydroxy(C₁-C₄)alkyl;        -   C1-C6 alkoxy; fluoro(C1-C6)alkoxy;        -   (C1-C6 alkyl)C(O)—;        -   (C1-C6 alkyl)NH—; (C1-C6 alkyl)₂N— (which includes, e.g.,            —NMe₂, —NMe(iPr));        -   —N*(R^(q′))₂, wherein R^(q)′—N*—R^(q)′ together form a            saturated ring having 5 or 6 ring atoms, in which 1 or 2            ring atoms (i.e., 1 or 2 ring atoms in addition to the N*            ring atom) is/are optionally a heteroatom independently            selected from NH, N(alkyl), O, or S (—N*(R^(q′))₂ includes            cyclic amino such as, e.g., pyrrolidinyl and morpholinyl);        -   formyl; formyl(C₁-C₄) alkyl; cyano; cyano(C₁-C₄) alkyl;        -   benzyl; benzyloxy;        -   heterocyclyl)-(C0-C6, e.g., C1-C6) alkyl, wherein the            heterocyclyl portion includes 5 or 6 ring atoms, in which 1            or 2 of the ring atoms is/are a heteroatom independently            selected from NH, N(alkyl), O, or S, and when said alkyl            portion is present (i.e., C1-C6), said alkyl portion serves            as the point of attachment to R1 (i.e., the            (heterocyclyl)-(C1-C6) alkyl is connected to R1 via the            alkyl portion); otherwise in the case of C0 alkyl (i.e., no            alkyl portion is present), a heterocyclyl carbon ring atom            serves as the point of attachment of the heterocyclyl to R1;        -   phenyl or heteroaryl including from 5-6 ring atoms, wherein            from 1-4 of the ring atoms is/are a heteroatom independently            selected from O, N, N—H, N—R^(q″), and S, each of which is            optionally substituted with from 1-3 R^(q″);        -   SO₂—(C1-C6)alkyl; SO—(C1-C6)alkyl; and        -   nitro;        -   in embodiments, R^(q) can be any one (or more) of the            substituents listed above and/or R^(q) can be any one or            more of the subsets of substituents listed above; e.g.,            R^(q) can be any one (or more) of the substituents that are            present, and/or any one (or more) of the substituents that            encompass those that are present, in the compounds described            herein;    -   each occurrence of R^(q″) is independently selected from the        group consisting of (beginning with halogen and through and        including nitro below):        -   halogen;        -   C1-C6 alkyl; fluoro(C1-C6)alkyl;        -   hydroxyl;        -   hydroxy(C₁-C₄)alkyl;        -   C1-C6 alkoxy; fluoro(C1-C6)alkoxy;        -   (C1-C6 alkyl)C(O)—;        -   (C1-C6 alkyl)NH—; (C1-C6 alkyl)₂N— (which includes, e.g.,            —NMe₂, —NMe(iPr));        -   formyl; formyl(C₁-C₄) alkyl; cyano; cyano(C₁-C₄) alkyl;        -   benzyl; benzyloxy;        -   heterocyclyl)-(C0-C6, e.g., C1-C6) alkyl, wherein the            heterocyclyl portion includes 5 or 6 ring atoms, in which 1            or 2 of the ring atoms is/are a heteroatom independently            selected from NH, N(alkyl), O, or S, and when said alkyl            portion is present (i.e., C1-C6), said alkyl portion serves            as the point of attachment to R1 (i.e., the            (heterocyclyl)-(C1-C6) alkyl is connected to R1 via the            alkyl portion); otherwise in the case of C0 alkyl (i.e., no            alkyl portion is present), a heterocyclyl carbon ring atom            serves as the point of attachment of the heterocyclyl to R1;        -   phenyl or heteroaryl including from 5-6 ring atoms, wherein            from 1-4 of the ring atoms is/are a heteroatom independently            selected from O, N, N—H, N—(C1-C6 alkyl), and S;            SO₂—(C1-C6)alkyl; SO—(C1-C6)alkyl; and nitro;        -   in embodiments, R^(q″) can be any one (or more) of the            substituents listed above and/or R^(q″) can be any one or            more of the subsets of substituents listed above; e.g.,            R^(q″) can be any one (or more) of the substituents that are            present, and/or any one (or more) of the substituents that            encompass those that are present, in the compounds described            herein;    -   U is selected from:        -   (i) ═CR^(r) (for purposes of clarification, in these            embodiments, the carbon atom in ═CR^(r) is doubly bonded to            a ring atom (e.g., ring carbon atom) of Cy, thereby forming            an exocyclic double bond, see, e.g., compounds F1-F7); or        -   (ii) —U′—C(R^(s))₂— or —C(R^(s))₂—U′—;    -   wherein:        -   R^(r) is hydrogen, F, C1-C6 alkyl, fluoro C1-C6 alkyl, C3-C6            cycloalkyl, C1-C6 alkoxy C1-C6 fluoroalkoxy, and cyano;        -   each occurrence of R^(s) is independently selected from H,            F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6            alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy C1-C6            fluoroalkoxy, and cyano; or        -   R^(s)—C—R^(s) together form C3-C6 cycloalkyl or heterocyclyl            including 3-6 ring atoms, in which one of the heterocyclyl            ring atoms is selected from O; S(O)m and NR^(u);        -   each occurrence of R^(u) is independently selected from H,            C1-C6 alkyl, —C(═O)H, —C(═O)R^(v), C(═O)O(C1-C6 alkyl),            C(═O)N(R^(w))₂, SO₂—R^(v), wherein R^(v) is selected from            C1-C6 alkyl, CH₂-(heteroaryl including 5-10 ring atoms),            CH₂—(C6-C10 aryl), and C6-C10 aryl; and each occurrence of            R^(w) is independently selected from H, C1-C6 alkyl,            CH₂-(heteroaryl including 5-10 ring atoms), CH₂—(C6-C10            aryl), and C6-C10 aryl (e.g., in embodiments, the aryl and            heteroaryl portion in R^(v) and R^(w) can be optionally            substituted, e.g., with one or more independently selected            substituents such as F, C1-C6 alkyl, fluoro C1-C6 alkyl,            C3-C6 cycloalkyl, C1-C6 alkoxy, C1-C6 fluoroalkoxy, or            cyano);        -   U′ is a bond; O; NR^(u); S(O)_(m) (m=0-2); CH₂; and U″—CH₂—;            wherein U″ is O; NR^(u); S(O)_(m) (m=0-2);    -   Cy is C4-C10 (e.g., C4-C8, C4-C6) cycloalkyl or saturated        heterocyclyl including 4-10 (e.g., 4-8, 4-6) ring atoms, each of        which is optionally substituted with from 1-3 R^(x) (wherein        each occurrence of R^(x) is independently selected from F, OH,        C1-C6 alkyl, fluoro C1-C6 alkyl, C3-C6 cycloalkyl, C1-C6 alkoxy        C1-C6 fluoroalkoxy, and cyano), in which from 1-3 heteroatoms        are independently selected from O, N—H, NR^(x′) (wherein R^(x′)        is defined as R^(q″)), and S(O)m (m=0-2); wherein when the        heterocyclyl contains a secondary amine as part of its        structure, then:        -   (i) V is linked through the nitrogen of the secondary amine            portion of the heterocyclyl; and        -   (ii) U is linked to Cy via a Cy ring carbon atom; wherein            the bond between U and the Cy ring carbon is a single or            double bond; and        -   (iii) V-Cy and Cy-U do no lead to 1,2 relationship (i.e. the            Cy ring carbon atom that is attached to U is not adjacent to            Cy ring nitrogen atom that is attached to V);        -   for purposes of clarification, the phrases “heterocyclyl            contains a secondary amine as part of its structure” and            “heterocyclyl that contains a secondary amine as part of its            structure” as used herein, mean that the parent heterocycle            includes as part of its structure a ring nitrogen atom of            the following formula:

-   -   -    in which the bonds intersected by the wavy lines indicate            bonds between the nitrogen atom and other ring atoms in the            parent heterocycle (the above-shown portion of the parent            heterocycle is sometimes referred to herein as the            “secondary amine” portion); other additional heteroatoms            (including nitrogens, including other secondary amine            nitrogens) can also be present in such a parent heterocycle,            however, when one (or more) secondary amine(s) is(are)            present in the parent heterocycle, it is the (or one of the)            secondary amine nitrogen atom(s) that serves as the point of            attachment of that heterocycle to variable V (i.e., V            replaces the H of the N—H in the parent heterocycle; see,            e.g., compounds F1-F7); examples of such parent heterocycles            include, without limitation, azetidine, pyrrolidine,            piperidine, azepane, diazepane, isoxazolidine,            thiazolidinone, imidazolidinone, pyrrolidinone,            azabicyclooctane (aka. tropane), azabicycloheptane,            azabicyclohexane; accordingly, examples of heterocyclyl that            contains a secondary amine as part of its structure include,            without limitation, azetidinyl, pyrrolidinyl, piperidinyl,            azepanyl, diazepanyl, isoxazolidinyl, thiazolidinonyl,            imidazolidinonyl, pyrrolidinonyl, azabicyclooctanyl (aka.            tropanyl), azabicycloheptanyl, azabicyclohexanyl;

    -   V is selected from:        -   (i) —V′—C(R^(y))₂— or —C(R^(y))₂—V′—; or        -   (ii) O, NR^(z), or S(O)m (m=0-2); or        -   (iii) —CH═CH—, C═O, C(R^(y))₂—C(═O), —C(═O)—C(R^(y))₂—,            —SO₂NRz^(t), NR^(z)SO₂, —C(═O)NR^(z), and NR^(z)C(═O);            wherein:            -   each occurrence of R^(y) is independently selected from                H, F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6                alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy C1-C6                fluoroalkoxy, and cyano; or            -   R^(y)—C—R^(y) together form C3-C6 cycloalkyl or                heterocyclyl including 3-6 ring atoms, in which one of                the heterocyclyl ring atoms is selected from O; S(O)m                and NR^(aa);            -   each occurrence of R^(z) and R^(aa) is independently                selected from H, C1-C6 alkyl, —C(═O)H, —C(═O)R^(v),                C(═O)O(C1-C6 alkyl), C(═O)N(R^(w))₂, SO₂—R^(v), wherein                R^(v) is selected from C1-C6 alkyl, CH₂-(heteroaryl                including 5-10 ring atoms), CH₂—(C6-C10 aryl), and                C6-C10 aryl; and each occurrence of R^(w) is                independently selected from H, C1-C6 alkyl,                CH₂-(heteroaryl including 5-10 ring atoms), CH₂—(C6-C10                aryl), and C6-C10 aryl;            -   V′ is a bond; O; NR^(u); S(O)_(m) (m=0-2);                —C(O)—O—(CR^(y) ₂)₀₋₂—, —(CR^(y) ₂)₀₋₂—O—C(O)—,                C(R^(y))₂, C(R^(y))₂—C(R^(y))₂; —(R^(y))₂—V″; and                V″—C(R^(y))₂—; wherein V″ is O; NR^(z); S(O)_(m)                (m=0-2); wherein each occurrence of R^(y) is                independently defined as above;            -   (in some embodiments, V′ is a bond; O; NR^(u); S(O)m                (m=0-2); —C(O)—O—(CH₂)₀₋₂—, —(CH₂)₀₋₂—O—C(O)—, CH₂;                —CH₂—V″; and V″—CH₂—;        -   wherein V″ is O; NR^(z); S(O)m (m=0-2));

    -   R2 is selected from H, F, Cl, CF₃, CF₂CF₃, CH₂CF₃, OCF₃, OCHF₂,        phenyl; substituted phenyl (e.g., phenyl substituted with from        1-3 substituents independently selected from F, OH, C1-C6 alkyl,        fluoro(C1-C6) alkyl C3-C6 cycloalkyl, NH₂, C1-C6 alkoxy, C1-C6        fluoroalkoxy, and cyano); thienyl; thiazolyl; and pyrazol-1-yl;        and

    -   R3 is H, F, or C1; or a salt (e.g., a pharmaceutically        acceptable salt) thereof.

In another aspect, a compound of the formula (I) is featured, in whichn=1, and each of the attendant definitions associated with n=1 (as wellas R2 and R3) can be as defined anywhere herein (in some embodiments,the definition of Ar/Het can further include 3,5-dimethylpyrazolyl).

In another aspect, a compound of the formula (I) is featured, in whichn=0, and each of the attendant definitions associated with n=0 (as wellas R2 and R3) can be as defined anywhere herein.

In a further aspect, the formula (I) compounds specifically describedherein (or a salt, e.g., a pharmaceutically acceptable salt thereof) arefeatured (e.g., compounds A1-A12, B1-B6, C1-C3, D1-D16, E1, E2, F1-F7,F8-F20, G1 and G2).

In one aspect, a composition (e.g., a pharmaceutical composition) isfeatured, which includes a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein anda pharmaceutically acceptable carrier. In some embodiments, thecomposition can include an effective amount of the compound or salt. Insome embodiments, the composition can further include an additionaltherapeutic agent.

In another aspect, a dosage form is featured, which includes from about0.05 milligrams to about 2,000 milligrams (e.g., from about 0.1milligrams to about 1,000 milligrams, from about 0.1 milligrams to about500 milligrams, from about 0.1 milligrams to about 250 milligrams, fromabout 0.1 milligrams to about 100 milligrams, from about 0.1 milligramsto about 50 milligrams, or from about 0.1 milligrams to about 25milligrams) of a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein.The dosage form can further include a pharmaceutically acceptablecarrier and/or an additional therapeutic agent.

The invention relates generally to inhibiting one (or more) HDACs (e.g.,HDAC1 or HDAC2; e.g., HDAC3) or more than one HDAC (e.g., HDAC1 andHDAC2; e.g., HDAC1 and HDAC3; e.g., HDAC2 or HDAC3; e.g., HDAC1, HDAC2,and HDAC 3) with a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein. Insome embodiments, the methods can include, e.g., contacting one (ormore) HDACs (e.g., HDAC1 or HDAC2; e.g., HDAC3) in a sample (e.g., acell or tissue) with a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein. Inother embodiments, the methods can include administering a compound offormula (I) or a salt (e.g., a pharmaceutically acceptable salt) thereofas defined anywhere herein to a subject (e.g., a mammal, such as ahuman). Accordingly, in yet another aspect, this invention includesmethods of screening for compounds that inhibit (e.g., selectivelyinhibit) one or more HDACs (e.g., HDAC1 or HDAC2; e.g., HDAC3, e.g.,HDAC1 and HDAC2; e.g., HDAC1 and HDAC3; e.g., HDAC2 or HDAC3; e.g.,HDAC1, HDAC2, and HDAC 3).

In one aspect, a method of selectively inhibiting HDAC3 is featured,which includes contacting an HDAC3 in a sample (e.g., a cell or tissue)with a compound of formula (I) or a salt (e.g., a pharmaceuticallyacceptable salt) thereof as defined anywhere herein; or administering acompound of formula (I) or a salt (e.g., a pharmaceutically acceptablesalt) thereof as defined anywhere herein to a subject (e.g., a mammal,such as a human).

In one aspect, a method of selectively inhibiting HDAC1 or HDAC2 (e.g.,HDAC1) is featured, which includes contacting HDAC1 or HDAC2 (e.g.,HDAC1) in a sample (e.g., a cell or tissue) with a compound of formula(I) or a salt (e.g., a pharmaceutically acceptable salt) thereof asdefined anywhere herein; or administering a compound of formula (I) or asalt (e.g., a pharmaceutically acceptable salt) thereof as definedanywhere herein to a subject (e.g., a mammal, such as a human).

In one aspect, a method of selectively inhibiting HDAC1, HDAC2, andHDAC3 is featured, which includes contacting HDAC1, HDAC2, and HDAC3 inone or more samples (e.g., a cell or tissue) with a compound of formula(I) or a salt (e.g., a pharmaceutically acceptable salt) thereof asdefined anywhere herein; or administering a compound of formula (I) or asalt (e.g., a pharmaceutically acceptable salt) thereof as definedanywhere herein to a subject (e.g., a mammal, such as a human).

In one aspect, methods of treating (e.g., controlling, relieving,ameliorating, alleviating, or slowing the progression of) or methods forpreventing (e.g., delaying the onset of or reducing the risk ofdeveloping) a disease or disorder mediated by HDAC1 or HDAC2 in asubject (e.g., a mammal, such as a human) in need thereof are featured,which include administering a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein tothe subject.

In one aspect, methods of treating (e.g., controlling, relieving,ameliorating, alleviating, or slowing the progression of) or methods forpreventing (e.g., delaying the onset of or reducing the risk ofdeveloping) a disease or disorder mediated by HDAC3 in a subject (e.g.,a mammal, such as a human) in need thereof are featured, which includeadministering a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein tothe subject.

In one aspect, methods of treating (e.g., controlling, relieving,ameliorating, alleviating, or slowing the progression of) or methods forpreventing (e.g., delaying the onset of or reducing the risk ofdeveloping) a disease or disorder mediated by two or more HDACs (e.g.,HDAC1 and HDAC2; e.g., HDAC1 and HDAC3; e.g., HDAC2 or HDAC3; e.g.,HDAC1, HDAC2, and HDAC 3) in a subject (e.g., a mammal, such as a human)in need thereof are featured, which include administering a compound offormula (I) or a salt (e.g., a pharmaceutically acceptable salt) thereofas defined anywhere herein to the subject.

In one aspect, featured are methods of treating (e.g., controlling,relieving, ameliorating, alleviating, or slowing the progression of) ormethods for preventing (e.g., delaying the onset of or reducing the riskof developing) a neurological disorder such as Friedreich's ataxia,myotonic dystrophy, spinal muscular atrophy, fragile X syndrome,Huntington's disease, spinocerebellar ataxia, Kennedy's disease,amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, andAlzheimer's disease; a cancer (e.g. cutaneous T cell lymphoma, B celllymphomas, and colorectal cancer); an inflammatory disease (e.g.,psoriasis, rheumatoid arthritis, and osteoarthritis); a memoryimpairment condition; post-traumatic stress disorder; a drug addiction;a Plasmodium falciparum infection (e.g., malaria) as well as otherparasite infections in a subject (e.g., a mammal, such as a human) inneed thereof, which include administering a compound of formula (I) or asalt (e.g., a pharmaceutically acceptable salt) thereof as definedanywhere herein to the subject.

In one aspect, a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein foruse in medicine is featured.

In one aspect, featured is a compound of formula (I) or a salt (e.g., apharmaceutically acceptable salt) thereof as defined anywhere herein forthe treatment of:

-   -   a disease or disorder mediated by HDAC1 or HDAC2;    -   a disease or disorder mediated by HDAC3;    -   A disease or disorder mediated by HDAC3 and HDAC1 or HDAC2;    -   A disease or disorder mediated by HDAC1 and HDAC2 and HDAC3;    -   a neurological disorder such as Friedreich's ataxia, myotonic        dystrophy, spinal muscular atrophy, fragile X syndrome,        Huntington's disease, spinocerebellar ataxia, Kennedy's disease,        amyotrophic lateral sclerosis, spinal and bulbar muscular        atrophy, and Alzheimer's disease; a cancer (e.g. cutaneous T        cell lymphoma, B cell lymphomas, and colorectal cancer); an        inflammatory disease (e.g., psoriasis, rheumatoid arthritis, and        osteoarthritis); a memory impairment condition; post-traumatic        stress disorder; a drug addiction; a Plasmodium falciparum        infection (e.g., malaria) as well as other parasite infections.

In one aspect, featured is a use of a compound of formula (I) or a salt(e.g., a pharmaceutically acceptable salt) thereof as defined anywhereherein, in the preparation of a medicament for the treatment of:

-   -   a disease or disorder mediated by HDAC1 or HDAC2;    -   a disease or disorder mediated by HDAC3;    -   A disease or disorder mediated by HDAC3 and HDAC1 or HDAC2;    -   A disease or disorder mediated by HDAC1 and HDAC2 and HDAC3;    -   a neurological disorder such as Friedreich's ataxia, myotonic        dystrophy, spinal muscular atrophy, fragile X syndrome,        Huntington's disease, spinocerebellar ataxia, Kennedy's disease,        amyotrophic lateral sclerosis, Niemann Pick disease, Pitt        Hopkins disease, spinal and bulbar muscular atrophy, and        Alzheimer's disease; a cancer (e.g. cutaneous T cell lymphoma, B        cell lymphomas, and colorectal cancer); an inflammatory disease        (e.g., psoriasis, rheumatoid arthritis, and osteoarthritis); a        memory impairment condition; post-traumatic stress disorder; a        drug addiction; an infectious disease such as HIV; a Plasmodium        falciparum infection (e.g., malaria) as well as other parasite        infections.

In some embodiments, the subject can be a subject in need thereof (e.g.,a subject identified as being in need of such treatment, such as asubject having, or at risk of having, one or more of the diseases orconditions described herein). Identifying a subject in need of suchtreatment can be in the judgment of a subject or a health careprofessional and can be subjective (e.g. opinion) or objective (e.g.measurable by a test or diagnostic method). In some embodiments, thesubject can be a mammal. In certain embodiments, the subject can be ahuman.

In one aspect, methods of making compounds described herein arefeatured. In embodiments, the methods include taking any one of theintermediate compounds described herein and reacting it with one or morechemical reagents in one or more steps to produce a compound of formula(I) or a salt (e.g., a pharmaceutically acceptable salt) thereof asdefined anywhere herein.

Some of the formula (I) compounds described herein have enhanced (e.g.,increased, e.g., increased by a factor of about 2 or more) stabilitiesin acid. In some embodiments, the formula (I) compounds have enhancedresistances to degradation, e.g., less than about 25% degradation (e.g.,less than about 20% degradation, less than about 15% degradation, orless than about 10% degradation) when exposed to acidic pH, e.g., acidicconditions intended to mimic those in the stomach, e.g., incubation(e.g., as a 10 μM solution) at 50° C. and at a pH of about 2.0 for aboutfour hours. The resistance of compounds to degradation or metabolism atacidic pH can be a useful feature for a pharmaceutical agent (e.g., adrug). Increased stability at low pH can allow, for example, processpreparation steps, such as salt formation, to occur without significantdegradation of the desired salt. In addition, it is preferable thatorally administered pharmaceuticals are stable to the acidic pH of thestomach. In some embodiments, compounds display enhanced stability whenexposed to acidic pH with stability half-lives greater than e.g. 12 h ore.g. 18 h or e.g 24 h at pH 2 and 50° C.

In some embodiments, the formula (I) compounds described hereinselectively inhibit HDAC3, e.g., selectively inhibit HDAC3 over HDAC1and HDAC2 (e.g exhibiting 5-fold or greater selectivity, e.g. exhibiting25-fold or greater selectivity). While not wishing to be bound bytheory, it is believed that HDAC3-selective inhibitors can increaseexpression of frataxin, and could therefore be useful in the treatmentof neurological conditions (e.g., neurological conditions associatedwith reduced frataxin expression, such as Friedreich's ataxia). It isalso believed that HDAC3 inhibition plays an important role in memoryconsolidation (McQuown S C et al, J Neurosci 31 764 (2011)). Selectiveinhibitors of HDAC3 could provide advantages for treatment ofneurological conditions over the use of broad-spectrum HDAC inhibitorsby reducing toxicities associated with inhibition of other HDACs. Suchspecific HDAC3 inhibitors would provide a higher therapeutic index,resulting in better tolerance by patients during chronic or long-termtreatment.

In some further embodiments, compounds selectively inhibit HDAC1 and/orHDAC2 (e.g exhibiting 5-fold or greater selectivity, e.g. exhibiting25-fold or greater selectivity).

In some embodiments, the formula (I) compounds described herein inhibitHDAC1, HDAC2 and HDAC3. While not wishing to be bound by theory, it isbelieved that HDAC3-selective inhibitors can increase expression offrataxin, and could therefore be useful in the treatment of neurologicalconditions (e.g., neurological conditions associated with reducedfrataxin expression, such as Friedreich's ataxia) and in neurons derivedfrom induced pluripotent stem cells generated from Friedreich's ataxiapatient cell line.

In some embodiments, the formula (I) compounds described herein havebeen shown to inhibit class I histone deacetylases and this inhibitionhas resulted in an in vitro increased frataxin mRNA expression inFriedreich's ataxia patient peripheral blood mononuclear cells (PBMCs).In other embodiments compounds of the invention have been shown toinhibit in vitro proliferation of colorectal cancer cells in adose-dependent fashion. In further embodiments compounds of theinvention have been demonstrated to increase long term memory in vivousing the novel object recognition paradigm.

In some embodiments, the formula (I) compounds described herein exhibitenhanced brain penetration. For example, brain/plasma ratios of greaterthan about 0.25 (e.g., greater than about 0.50, greater than about 1.0,greater than about 1.5, or greater than about 2.0) are observed whenmice are dosed with some of the formula (I) compounds described herein.Such compounds are therefore expected to be particularly suitable fortherapies targeting the brain (e.g., neurological conditions such asFriedreich's ataxia, myotonic dystrophy, spinal muscular atrophy,fragile X syndrome, Huntington's disease, spinocerebellar ataxia,Kennedy's disease, amyotrophic lateral sclerosis, spinal and bulbarmuscular atrophy, and Alzheimer's disease; a memory impairmentcondition; post-traumatic stress disorder; a drug addiction).

In some embodiments, the formula (I) compounds described hereinselectively inhibit HDAC3, e.g., selectively inhibit HDAC3 over HDAC1and HDAC2 (e.g exhibiting 5-fold or greater selectivity, e.g. exhibiting25-fold or greater selectivity) and exhibit enhanced brain penetration(e.g., as described above).

In some embodiments, the formula (I) compounds described hereinselectively inhibit HDAC1 and/or HDAC2, e.g., selectively inhibit HDAC1and/or HDAC2 over HDAC3 (e.g exhibiting 5-fold or greater selectivity,e.g. exhibiting 25-fold or greater selectivity) and exhibit enhancedbrain penetration (e.g., as described above).

Embodiments can include one or more of the following features.

[I] n is 1 (i.e., in which Z is R₁—X—Ar/Het). Embodiments in which n is1 can include one or more of the following features described throughoutsections [A] through [F] below.

[A] Variable X

[1] In some embodiments, X is —Y—[C(R^(a))₂]_(a)-A-[C(R^(b))₂]_(b)—B—.Embodiments can also include one or more of the features described in[a]-[d] below.

[a]

A is a bond and/or B is a bond (in some embodiments, each of A and B isa bond; or one of A and B (e.g., B) is a bond, and the other of A and B(e.g., A) is other than a bond, e.g., O or NR^(f), e.g., 0; inembodiments, each of A and B is other than S(O)_(m)).

Each occurrence of R^(a) and R^(b) (when present) is independentlyselected from H, F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy C1-C6 fluoroalkoxy, andcyano.

Each occurrence of R^(a) and R^(b) (when present) is independentlyselected from H, F, C1-C6 alkyl, and C3-C6 cycloalkyl.

Each occurrence of R^(a) and R^(b) (when present) is H.

One or more (e.g., one) of the following apply:

-   -   any two R^(a), together with the carbons to which each is        attached, together form C3-C6 cycloalkyl or heterocyclyl        including 3-6 ring atoms, in which one of the heterocyclyl ring        atoms is selected from O; S(O), and NR^(g); in these        embodiments, any remaining occurrences of R^(a) and any        occurrence of R^(b) are each independently defined according to        any one or more of the preceding or following definitions        pertaining to R^(a) and R^(b); or    -   one R^(a) and one R^(b), together with the carbons to which each        is attached, form C3-C6 cycloalkyl or heterocyclyl including 3-6        ring atoms, in which one of the heterocyclyl ring atoms is        selected from O; S(O), and NR^(g); in these embodiments, the        other R^(a), the other R^(b), and any other remaining        occurrences of R^(a) and R^(b) are each independently defined        according to any one or more of the preceding or following        definitions pertaining to R^(a) and R^(b); or    -   any two R^(b), together with the carbons to which each is        attached, form C3-C6 cycloalkyl or heterocyclyl including 3-6        ring atoms, in which one of the ring atoms is selected from O;        S(O)_(m) and NR^(g); in these embodiments, each occurrence of        R^(a) and any other remaining occurrences of R^(b) are each        independently defined according to any one or more of the        preceding definitions pertaining to R^(a) and R^(b).

[b]

In some embodiments, Y is CR^(c)═CR^(d) (in some embodiments, the doublebond between CR^(c) and CR^(d) has the trans configuration; in otherembodiments, the double bond between CR^(c) and CR^(d) has the cisconfiguration). Embodiments can include one or more of the followingfeatures.

The double bond between CR^(c) and CR^(d) has the trans configuration.Each of R^(c) and R^(d) is, independently, selected from H, F, OH, C1-C6alkyl, C3-C5 cycloalkyl, NH₂, OCO—(C1-C6 alkyl), OCO—(C3-C5 cycloalkyl),C1-C6 alkoxy, C1-C6 fluoroalkoxy, and cyano. In certain embodiments,each of R^(c) and R^(d) is H.

A is a bond and/or B is a bond (in some embodiments, each of A and B isa bond).

Each of R^(a) and R^(b) can be as defined anywhere herein (see, forexample, the R^(a) and R^(b) features described above in section[I][A][1][a]).

a is 1 or 2 (e.g., 1). b is 0 or 1 (e.g., 0).

a is 1 or 2, e.g., 1; and b is 0 or 1, e.g., 0 (in further embodiments,each of A and B is also a bond.

b is 0 (in embodiments, a is 1 or 2, e.g., 1; in further embodiments,each of A and B is also a bond).

X is —CH═CH—C(R^(a))₂—. In certain embodiments, each R^(a) is hydrogen.In other embodiments, each R^(a) is a substituent other than hydrogen(e.g., C1-C6 alkyl), and each R^(a) can be the same or different, e.g.,the same. For example, each R^(a) can be the same C1-C6 alkyl, such asCH₃.

X is —CH═CH—CH(R^(a))—. In certain embodiments, R^(a) is hydrogen; inother embodiments, R^(a) is a substituent other than hydrogen (e.g., asdescribed above).

X is —CH═CH—C(R^(a))₂—C(R^(a))₂. In certain embodiments, each R^(a) ishydrogen. In other embodiments, each R^(a) is a substituent other thanhydrogen (e.g., C1-C6 alkyl), and each R^(a) can be the same ordifferent, e.g., the same. For example, each R^(a) can be the same C1-C6alkyl, such as CH₃. In still other embodiments, in one germinal pair ofR^(a)′s, each R^(a) is hydrogen; and in the other germinal pair ofR^(a)′s, each R^(a) is a substituent other than hydrogen (e.g., asdescribed above).

X is —CH═CHCH(R^(a))CH(R^(a)). In certain embodiments, each R^(a) ishydrogen; in other embodiments, each R^(a) is a substituent other thanhydrogen; in still other embodiments, one R^(a) is hydrogen, and theother is a substituent other than hydrogen.

For example, X is —CH═CH—CH₂— or —CH═CH—CH₂—CH₂— (e.g., in the foregoingembodiments, the double bond can have the trans configuration; andfurther each of A and B can be a bond). In certain embodiments, X is—CH═CH—CH₂— (e.g., trans).

[c]

In some embodiments, Y is O, NR^(e), or S(O)_(m); e.g., Y is O orNR^(e). Embodiments can include one or more of the following features.

Y is O.

Y is NR^(e) (e.g., R^(e) is C1-C6 alkyl).

A is a bond and/or B is a bond (in some embodiments, each of A and B isa bond).

Each of R^(a) and R^(b) can be as defined anywhere herein (see, forexample, the R^(a) and R^(b) features described above in section[I][A][1][a]).

a is 2 or 3 (e.g., 2) and b is optionally other than 0 (e.g., 1 or 2);in embodiments, A is a bond; or A is other than a bond, e.g., O orNR^(f), e.g., O; and B is a bond. Some examples are provided below:

-   -   a is 2 or 3 (e.g., 2), b is 0; and each of A and B is a bond.    -   a is 2 or 3 (e.g., 2), b is other than 0 (e.g., 1 or 2), and        each of A and B is a bond.    -   a is 2 or 3 (e.g., 2), b is other than 0 (e.g., 2 or 3), A is        other than a bond, e.g., O or NR^(f), e.g., O, and B is a bond.

For example, X is —O—(CH₂)_(2-3(e.g., 2)) or—N(CH₃)—(CH₂)_(2-3(e.g., 2)).

[d]

In some embodiments, Y is a bond. Embodiments can include one or more ofthe following features.

A is a bond, O, or NR^(e) (e.g., A is a bond or O, e.g., A is a bond)and/or B is a bond. In certain embodiments, A is a bond and B is a bond.

Each of R^(a) and R^(b) can be as defined anywhere herein (see, forexample, the R^(a) and R^(b) features described above in section[I][A][1][a]).

b is 0 (in embodiments, a can be 1, 2, or 3 (e.g., 1) and one or more ofthe following can apply: A is a bond, A is other than a bond, such as O;B is a bond, each of R^(a) is H; e.g., A is a bond, a is 1, B is a bond;e.g., X is CH₂).

b is 1, 2, or 3 (in embodiments, a can be 1, 2, or 3 and one or more ofthe following can apply: A is a bond, A is other than a bond, such as O;B is a bond, each of R^(a) is H, each of R^(b) is H). In certain ofthese embodiments, X has a span of not more than 4 atoms.

[2] In some embodiments, X is a bond.

[B] Variables R4 and R5

In some embodiments, each of R4 and R5 is H.

[C] Variable Ar/Het

[1]

In some embodiments, Ar/Het is 5 membered heteroaromatic chosen frompyrazolyl, thiazolyl, oxazolyl, imidazolyl, thienyl, furanyl,isoxazolyl, isothiazolyl, thiadiazolyl, oxadiazolyl, and 1,2,4-triazolyl(in some embodiments, the definition of Ar/Het can further include3,5-dimethylpyrazolyl); or a bicyclic 8-, 9-, or 10-memberedheteroaromatic chosen from benzofuranyl, benzothienyl, benzothiazolyl,indolyl, indazolyl, quinolonyl, and naphtyridinyl (in some embodiments,Ar/Het is other than furanyl and 1,2,4-triazolyl. In certainembodiments, Ar/Het is other than furanyl; in certain embodiments,Ar/Het is other than 1,2,4-triazolyl).

In some embodiments, Ar/Het is 5 membered heteroaromatic selected frompyrazolyl, thiazolyl, oxazolyl, imidazolyl, isoxazolyl, isothiazolyl,thiadiazolyl, oxadiazolyl, and 1,2,4-triazolyl (in some embodiments,Ar/Het is other than furanyl and 1,2,4-triazolyl. In certainembodiments, Ar/Het is other than furanyl; in certain embodiments,Ar/Het is other than 1,2,4-triazolyl). In certain embodiments, Ar/Het ispyrazolyl. In some embodiments, the definition of Ar/Het can furtherinclude 3,5-dimethylpyrazolyl.

In some embodiments, Ar/Het is other than furanyl and 1,2,4-triazolyl.In certain embodiments, Ar/Het is other than furanyl. In certainembodiments, Ar/Het is other than 1,2,4-triazolyl.

[2]

In some embodiments, Ar/Het is a bicyclic 8-, 9-, or 10-memberedheteroaryl selected from the group consisting of benzofuranyl,benzothienyl, benzothiazolyl, indolyl, indazolyl, quinolonyl,naphtyridinyl, indolizinyl, pyrrolopyrimidinyl, pyrazolopyridinyl,imidazopyridinyl, imidazopyridazinyl, triazolopyridinyl,imidazothiazolyl, imidazooxazolyl, triazolothiazolyl, andtriazolooxazolyl.

In some embodiments, Ar/Het is a bicyclic 8-, 9-, or 10-memberedazabridged hetero aromatic such as indolizinyl, pyrrolopyrimidinyl,pyrazolopyridinyl, imidazopyridinyl, imidazopyridazinyl,triazolopyridinyl, imidazothiazolyl, imidazooxazolyl,1,2,4-triazolothiazolyl, and 1,2,4-triazolooxazolyl.

[D] Variable R1

[1]

In some embodiments, R1 is C6-C10 aryl, which is optionally substitutedwith from 1-3 R^(o). In certain embodiments, R1 is phenyl or naphthyl(e.g., phenyl), which is optionally substituted with from 1-3 R^(o) (inembodiments, each R^(o) is independently selected from F, OH, C1-C6alkyl, fluoro(C1-C6) alkyl C3-C6 cycloalkyl, NH₂, C1-C6 alkoxy, C1-C6fluoroalkoxy, and cyano).

In other embodiments, R1 is C8-C10 aryl, which contains a phenyl ringfused to a non-aromatic ring and which is optionally substituted withfrom 1-3 R^(o) (e.g., optionally substituted indanyl or tetralinyl).

[2]

In some embodiments, R1 is monocyclic or bicyclic heteroaryl includingfrom 5-10 ring atoms, which is optionally substituted with from 1-3R^(o); wherein from 1-4 of the ring atoms is/are a heteroatomindependently selected from O, N, N—H, N—R^(o), and S.

In certain embodiments, R1 is monocyclic heteroaryl, such as pyridyl.

In other embodiments, R1 is bicyclic heteroaryl, such as those that arefully aromatic such as indolyl and the like.

In still other embodiments, R1 is bicyclic heteroaryl that contains abridgehead nitrogen ring atom and optionally other heteroatom ringatoms, such as indolizinyl, pyrrolopyrimidinyl, pyrazolopyridinyl,imidazopyridinyl, imidazopyriazinyl, triazolopyridinyl,imidazothiazolyl, imidazooxazolyl.

Other examples of R1 heteroaryl groups include, without limitation,pyrazolyl, pyrrolyl, 2-oxo-indolyl, quinolinyl, isoquinolinyl,tetrahydro-isoquinolinyl, benzofuranyl, benzodioxanyl, benzodioxolyl(aka. methylenedioxyphenyl) and corresponding difluoro (CF₂) analog,thiazolyl, 2-oxopyridinyl, pyridinyl N-oxide, pyrimidinyl, thienyl,furanyl, oxazolyl, isoxazolyl, pyridazinyl, imidazolyl, pyrazinyl,isothiazolyl, 1,2-thiazinyl-1,1-dioxide, benzimidazolyl, thiadiazolyl,benzopyranyl, benzothiazolyl, benzotriazolyl, benzoxazolyl,benzothienyl, oxadiazolyl, triazolyl, tetrazolyl, dioxoindolyl (isatin),phthalimido and the dihydro and tetrahydro congeners of the fullyunsaturated ring systems.

[3]

In some embodiments, R1 is heterocyclyl including from 4-10 ring atoms,which is optionally substituted with from 1-3 R^(o); wherein from 1-4 ofthe ring atoms is/are a heteroatom independently selected from O, N,N—H, N—R^(o), and S (e.g., bicyclic heterocyclyl containing a bridgeheadnitrogen ring atom and optionally other heteroatom ring atoms).

Examples of R1 heterocyclyl groups include, without limitation,piperidinyl, morpholinyl, pyrrolidinyl, azetidinyl, azepanyl,isoxazolidinyl, oxazolidinyl, thiazolidinyl, imidazolinyl,quinuclidinyl, isothiazolidinyl, tetrahydrofuranyl, tetrahydropyranyl,thiamorpholinyl, thiamorpholinyl sulfoxide, thiamorpholinyl sulfone,dioxanyl, tropanyl and other bridged bicyclic amines, quiniclidinyl.

[4]

In some embodiments, R1 is H.

[E] Variables R2 and R3

[1]

In some embodiments, R2 is a substituent other than hydrogen (e.g.,phenyl, substituted phenyl, thienyl, thiazolyl, and pyrazol-1-yl), andR3 is hydrogen. In certain embodiments, the compounds can exhibitselectivity for HDAC 1 and/or 2.

[2]

In some embodiments, R2 is hydrogen, and R3 is a substituent other thanhydrogen (e.g., fluoro). In certain embodiments, the compounds canexhibit selectivity for HDAC 3.

[3]

In some embodiments, each of R2 and R3 is hydrogen.

[F] Non-Limiting Combinations of [I][A] through [I][E] (i.e., n=1)

In some embodiments, one or more of the features described in one ormore of [A][1][a], [A][1][b], [A][1][c], and [A][1][d] can be combinedwith: the features described in [B], and/or one or more of the featuresdescribed in one or both of [C][1] and [C][2], and/or one or more of thefeatures described in one or more of [D][1], [D][2], [D][3], and [D][4],and/or one or more of the features described in one or more of [E][1],[E][2], and [E][3].

In some embodiments, one or more of the features described in one ormore of [A][1][a], [A][1][b], [A][1][c], and [A][1][d] can be combinedwith: the features described in [B], and one or more of the featuresdescribed in one or both of [C][1] and [C][2], and one or more of thefeatures described in one or more of [D][1], [D][2], [D][3], and [D][4],and one or more of the features described in one or more of [E][1],[E][2], and [E][3].

In some embodiments, one or more of the features described in one ormore of [A][1][a], [A][1][b], [A][1][c], and [A][1][d] can be combinedwith: the features described in [B], and one or more of the featuresdescribed in [C][1], and one or more of the features described in one ormore of [D][1], [D][2], [D][3], and [D][4], and one or more of thefeatures described in one or more of [E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in one ormore of [A][1][a], [A][1][b], [A][1][c], and [A][1][d] can be combinedwith: the features described in [B], and one or more of the featuresdescribed in one or both of [C][1] and [C][2], and one or more of thefeatures described in one or both of [D][1] and [D][4] (e.g., [D][1]),and one or more of the features described in one or more of [E][1],[E][2], and [E][3].

In some embodiments, one or more of the features described in one ormore of [A][1][a], [A][1][b], [A][1][c], and [A][1][d] can be combinedwith: the features described in [B], and one or more of the featuresdescribed in [C][1], and one or more of the features described in one orboth of [D][1] and [D][4] (e.g., [D][1]), and one or more of thefeatures described in one or more of [E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in [A][1][b]can be combined with: the features described in [B], and one or more ofthe features described in one or both of [C][1] and [C][2], and one ormore of the features described in one or more of [D][1], [D][2], [D][3],and [D][4], and one or more of the features described in one or more of[E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in [A][1][b]can be combined with: the features described in [B], and one or more ofthe features described in [C][1], and one or more of the featuresdescribed in one or more of [D][1], [D][2], [D][3], and [D][4], and oneor more of the features described in one or more of [E][1], [E][2], and[E][3].

In some embodiments, one or more of the features described in [A][1][b]can be combined with: the features described in [B], and one or more ofthe features described in one or both of [C][1] and [C][2], and one ormore of the features described in [D][1], and one or more of thefeatures described in one or more of [E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in [A][1][b]can be combined with: the features described in [B], and one or more ofthe features described in [C][1], and one or more of the featuresdescribed in [D][1], and one or more of the features described in one ormore of [E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in [A][1][d]can be combined with: the features described in [B], and one or more ofthe features described in one or both of [C][1] and [C][2], and one ormore of the features described in one or more of [D][1], [D][2], [D][3],and [D][4], and one or more of the features described in one or more of[E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in [A][1][d]can be combined with: the features described in [B], and one or more ofthe features described in [C][1], and one or more of the featuresdescribed in one or more of [D][1], [D][2], [D][3], and [D][4], and oneor more of the features described in one or more of [E][1], [E][2], and[E][3].

In some embodiments, one or more of the features described in [A][1][d]can be combined with: the features described in [B], and one or more ofthe features described in one or both of [C][1] and [C][2], and one ormore of the features described in one or both of [D][1] and [D][4], andone or more of the features described in one or more of [E][1], [E][2],and [E][3].

In some embodiments, one or more of the features described in [A][1][d]can be combined with: the features described in [B], and one or more ofthe features described in [C][1], and one or more of the featuresdescribed in one or both of [D][1] and [D][4], and one or more of thefeatures described in one or more of [E][1], [E][2], and [E][3].

In some embodiments, one or more of the features described in one ormore of [A][2] can be combined with: the features described in [B],and/or one or more of the features described in one or both of [C][1]and [C][2] (e.g., [C][2]) and/or one or more of the features describedin one or more of [D][1], [D][2], [D][3], and [D][4] (e.g., [D][4])and/or one or more of the features described in one or more of [E][1],[E][2], and [E][3].

[II] n is 0 (i.e., in which A is Z is R₁—V-Cy-U—Ar′/Het′). Embodimentsin which n is 0 can include one or more of the following featuresdescribed throughout sections [AA] through [GG] below.

[AA] Variable Ar′/Het′

[1]

In some embodiments, Ar′/Het′ is phenyl, pyridyl, or pyrimidinyl, eachof which is optionally substituted with from 1-3 R^(p); provided thatthe point of connection on said phenyl, pyridyl, or pyrimidinyl to U(i.e., the connection U—Ar′/Het′ in formula I) and the point ofconnection on said phenyl, pyridyl, or pyrimidinyl to the amide carbonyl(i.e., the connection Ar′/Het′-C(═O) in formula I) do not result in1,2-relation to one another on said phenyl, pyridyl, or pyrimidinyl(i.e., the points of connection to U and C(O) on said phenyl, pyridyl,or pyrimidinyl are not ortho with respect to one another).

In some embodiments, Ar′/Het′ is phenyl, pyridyl, or pyrimidinyl, eachof which is optionally substituted with from 1-3 R^(p); wherein thepoint of connection on said phenyl, pyridyl, or pyrimidinyl to U (i.e.,the connection U—Ar′/Het′ in formula I) and the point of connection onsaid phenyl, pyridyl, or pyrimidinyl to the amide carbonyl (i.e., theconnection Ar′/Het′-C(═O) in formula I) results in a 1,4-relation to oneanother on said phenyl, pyridyl, or pyrimidinyl (i.e., the points ofconnection to U and C(O) on said phenyl, pyridyl, or pyrimidinyl arepara with respect to one another).

In some embodiments, Ar′/Het′ is phenyl, which is optionally substitutedwith from 1-3 R^(p); provided that the point of connection on saidphenyl to U (i.e., the connection U—Ar′/Het′ in formula I) and the pointof connection on said phenyl to the amide carbonyl (i.e., the connectionAr′/Het′-C(═O) in formula I) does not result in a 1,2-relation to oneanother on said phenyl (i.e., the points of connection to U and C(O) onsaid phenyl are not ortho with respect to one another).

In some embodiments, Ar′/Het′ is phenyl, which is optionally substitutedwith from 1-3 R^(p); wherein the point of connection on said phenyl to U(i.e., the connection U—Ar′/Het′ in formula I) and the point ofconnection on said phenyl to the amide carbonyl (i.e., the connectionAr′/Het′-C(═O) in formula I) results in a 1,4-relation to one another onsaid phenyl (i.e., the points of connection to U and C(O) on said phenylare para with respect to one another).

[2]

In some embodiments, Ar′/Het′ is a 5-membered heteroaryl selected frompyrazolyl, pyrrolyl, thiazolyl, thienyl, furanyl, imidazolyl, oxazolyl,oxadiazolyl, thiadiazolyl, isoxazolyl, isothiazolyl, each of which isoptionally substituted with from 1-3 R^(p); provided that the point ofconnection on said 5-membered heteroaryls to U (i.e., the connectionU—Ar′/Het′ in formula I) and the point of connection on said 5-memberedheteroaryls to the amide carbonyl (i.e., the connection Ar′/Het′-C(═O)in formula I) do not result in 1,2-relation to one another on said5-membered heteroaryls (i.e., the points of connection to U and C(O) onsaid 5-membered heteroaryl are not adjacent to one another).

[3]

In some embodiments, Ar′/Het′ is a 8-, 9- or 10-membered bicyclicheteroaryl selected from benzothienyl, benzofuranyl, benzothioazolyl,benzoxazolyl, indolyl, isoindolonyl, indolizinyl, pyrrolopyrimidinyl,pyrazolopyridinyl, imidazopyridinyl, imidazopyridazinyl,triazolopyridinyl, imidazothiazolyl, imidazooxazolyl, quinolinyl, andnaphthyridinyl; each of which is optionally substituted with from 1-3R^(p).

In certain embodiments, Ar′/Het′ is a 8-, 9- or 10-membered bicyclicheteroaryl selected from indolizinyl, pyrrolopyrimidinyl,pyrazolopyridinyl, imidazopyridinyl, imidazopyridazinyl,triazolopyridinyl, imidazothiazolyl, and imidazooxazolyl; each of whichis optionally substituted with from 1-3 R^(p).

[BB] Variable Cy

[1]

In some embodiments, Cy is a saturated heterocyclyl including 4-10(e.g., 4-8, 4-6) ring atoms, each of which is optionally substitutedwith from 1-3 R^(x) (wherein each occurrence of R^(x) is independentlyselected from F, OH, C1-C6 alkyl, fluoro C1-C6 alkyl, C3-C6 cycloalkyl,C1-C6 alkoxy C1-C6 fluoroalkoxy, and cyano), in which from 1-3heteroatoms are independently selected from O, N—H, NR^(x′) (whereinR^(x′) is defined as R^(q″)), and S(O)_(m) (m=0-2); wherein when theheterocyclyl contains a secondary amine as part of its structure, then:

-   -   (i) V is linked through the nitrogen of the secondary amine        portion of the heterocyclyl; and    -   (ii) U is linked to Cy via a Cy ring carbon atom; wherein the        bond between U and the Cy ring carbon is a single or double        bond; and    -   (iii) V-Cy and Cy-U do not lead to 1,2 relationship (i.e. the Cy        ring carbon atom that is attached to U is not adjacent to Cy        ring nitrogen atom that is attached to V).

In certain embodiments, Cy is a heterocyclyl that contains a secondaryamine as part of its structure.

In certain embodiments, Cy is azetidinyl, pyrrolidinyl, piperidinyl,azepanyl, diazepanyl, isoxazolidinyl, thiazolidinonyl, imidazolidinonyl,pyrrolidinonyl, azabicyclooctyl (aka. tropanyl), azabicycloheptanyl, orazabicyclohexanyl.

In certain embodiments, Cy is azetidinyl, pyrrolidinyl or piperidinyl(e.g., azetidinyl or piperidinyl).

[2]

In some embodiments, Cy is cycloalkyl (e.g., cyclobutyl, cyclopentyl,cyclohexyl).

[CC] Variable V

In some embodiments, V is —V′—C(R^(y))₂— or —C(R^(y))₂—V′—.

In some embodiments, each occurrence of R^(y) is independently selectedfrom H, F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6 alkyl),OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy C1-C6 fluoroalkoxy, and cyano.

In certain embodiments, each occurrence of R^(y) is independentlyselected from H, F, C1-C6 alkyl, and C3-C6 cycloalkyl.

In certain embodiments, each occurrence of R^(y) is H.

In some embodiments, V′ is a bond.

[DD] Variable U

In some embodiments, U is ═CR^(r). R^(r) is hydrogen.

In certain embodiments, U is —U′—C(R^(s))₂— or —C(R^(s))₂—U′—.

In certain embodiments, each occurrence of R^(s) is independentlyselected from H, F, OH, C1-C6 alkyl, C3-C6 cycloalkyl, NH₂, OCO—(C1-C6alkyl), OCO—(C3-C6 cycloalkyl), C1-C6 alkoxy C1-C6 fluoroalkoxy, andcyano.

In certain embodiments, each occurrence of R^(s) is independentlyselected from H, F, C1-C6 alkyl, and C3-C6 cycloalkyl.

In certain embodiments, each occurrence of R^(s) is H.

In some embodiments, U′ is a bond.

[EE] Variable R1

[1]

In some embodiments, R1 is C6-C10 aryl, which is optionally substitutedwith from 1-3 R^(q). In certain embodiments, R1 is phenyl or naphthyl(e.g., phenyl), which is optionally substituted with from 1-3 R^(q) (inembodiments, each R^(q) is independently selected from F, OH, C1-C6alkyl, fluoro(C1-C6) alkyl C3-C6 cycloalkyl, NH₂, C1-C6 alkoxy, C1-C6fluoroalkoxy, and cyano).

[2]

In some embodiments, R1 is monocyclic or bicyclic heteroaryl includingfrom 5-10 ring atoms, which is optionally substituted with from 1-3R^(q); wherein from 1-4 of the ring atoms is/are a heteroatomindependently selected from O, N, N—H, N—R^(q), and S.

In certain embodiments, R1 is monocyclic heteroaryl, such as pyridyl.

In other embodiments, R1 is bicyclic heteroaryl, such as those that arefully aromatic such as indolyl and the like.

In still other embodiments, R1 is bicyclic heteroaryl that contains abridgehead nitrogen ring atom and optionally other heteroatom ringatoms, such as indolizinyl, pyrrolopyrimidinyl, pyrazolopyridinyl,imidazopyridinyl, imidazopyriazinyl, triazolopyridinyl,imidazothiazolyl, imidazooxazolyl.

Other examples of R1 heteroaryl groups include, without limitation,pyrazolyl, pyrrolyl, 2-oxo-indolyl, quinolinyl, isoquinolinyl,tetrahydro-isoquinolinyl, benzofuranyl, benzodioxanyl, benzodioxolyl(aka. methylenedioxyphenyl) and corresponding difluoro (CF₂) analog,thiazolyl, 2-oxopyridinyl, pyridinyl N-oxide, pyrimidinyl, thienyl,furanyl, oxazolyl, isoxazolyl, pyridazinyl, imidazolyl, pyrazinyl,isothiazolyl, 1,2-thiazinyl-1,1-dioxide, benzimidazolyl, thiadiazolyl,benzopyranyl, benzothiazolyl, benzotriazolyl, benzoxazolyl,benzothienyl, oxadiazolyl, triazolyl, tetrazolyl, dioxoindolyl (isatin),phthalimido and the dihydro and tetrahydro congeners of the fullyunsaturated ring systems.

[3]

In some embodiments, R1 is heterocyclyl including from 4-10 ring atoms,which is optionally substituted with from 1-3 R^(q); wherein from 1-4 ofthe ring atoms is/are a heteroatom independently selected from O, N,N—H, N—R^(q), and S (e.g., bicyclic heterocyclyl containing a bridgeheadnitrogen ring atom and optionally other heteroatom ring atoms).

Examples of R1 heterocyclyl groups include, without limitation,piperidinyl, morpholinyl, pyrrolidinyl, azetidinyl, azepanyl,isoxazolidinyl, oxazolidinyl, thiazolidinyl, imidazolinyl,quinuclidinyl, isothiazolidinyl, tetrahydrofuranyl, tetrahydropyranyl,thiamorpholinyl, thiamorpholinyl sulfoxide, thiamorpholinyl sulfone,dioxanyl, tropanyl and other bridged bicyclic amines, quiniclidinyl.

[4]

In some embodiments, R1 is H.

[FF] Variables R2 and R3

[1]

In some embodiments, R2 is a substituent other than hydrogen (e.g.,phenyl, substituted phenyl, thienyl, thiazolyl, and pyrazol-1-yl), andR3 is hydrogen. In certain embodiments, the compounds can exhibitselectivity for HDAC 1 and/or 2.

[2]

In some embodiments, R2 is hydrogen, and R3 is a substituent other thanhydrogen (e.g., fluoro). In certain embodiments, the compounds canexhibit selectivity for HDAC 3.

[3]

In some embodiments, each of R2 and R3 is hydrogen.

[GG] Non-Limiting Combinations of [II][AA] Through [II][FF] (i.e., n=0)

In some embodiments, one or more of the features described in one ormore of [AA][1], [AA][2], and [AA][3] can be combined with: one or moreof the features described in [DD], and/or one or more of the featuresdescribed in [CC], and/or one or more of the features described in oneor both of [BB][1] and [BB][2], and/or one or more of the featuresdescribed in one or more of [EE][1], [EE][2], [EE][3], and [EE][4],and/or one or more of the features described in one or more of [FF][1],[FF][2], and [FF][3].

In some embodiments, one or more of the features described in one ormore of [AA][1], [AA][2], and [AA][3] can be combined with: one or moreof the features described in [DD], and one or more of the featuresdescribed in [CC], and one or more of the features described in one orboth of [BB][1] and [BB][2], and one or more of the features describedin one or more of [EE][1], [EE][2], [EE][3], and [EE][4], and one ormore of the features described in one or more of [FF][1], [FF][2], and[FF][3].

In some embodiments, one or more of the features described in [AA][1],can be combined with: one or more of the features described in [DD], andone or more of the features described in [CC], and one or more of thefeatures described in one or both of [BB][1] and [BB][2], and one ormore of the features described in one or more of [EE][1], [EE][2],[EE][3], and [EE][4], and one or more of the features described in oneor more of [FF][1], [FF][2], and [FF][3].

In some embodiments, one or more of the features described in one ormore of [AA][1], [AA][2], and [AA][3] can be combined with: one or moreof the features described in [DD], and one or more of the featuresdescribed in [CC], and one or more of the features described in [BB][1],and one or more of the features described in one or more of [EE][1],[EE][2], [EE][3], and [EE][4], and one or more of the features describedin one or more of [FF][1], [FF][2], and [FF][3].

In some embodiments, one or more of the features described in one ormore of [AA][1], [AA][2], and [AA][3] can be combined with: one or moreof the features described in [DD], and one or more of the featuresdescribed in [CC], and one or more of the features described in one orboth of [BB][1] and [BB][2], and one or more of the features describedin [EE][2], and one or more of the features described in one or more of[FF][1], [FF][2], and [FF][3].

In some embodiments, one or more of the features described in [AA][1]can be combined with: one or more of the features described in [DD], andone or more of the features described in [CC], and one or more of thefeatures described in [BB][1], and one or more of the features describedin [EE][2], and one or more of the features described in one or more of[FF][1], [FF][2], and [FF][3].

In certain embodiments, n is 1, and X is—Y—[C(R^(a))₂]_(a)-A-[C(R^(b))₂]_(b)—B—.

In certain embodiments, n is 1, and X is—Y—[C(R^(a))₂]_(a)-A-[C(R^(b))₂]_(b)—B—, and Y is CR^(c)═CR^(d).Embodiments can include any one or more of the features describedherein. For example, one or both of the following: R1 is C6-C10 aryl(e.g., phenyl), which is optionally substituted with from 1-3 R^(o); andAr/Het is 5 membered heteroaromatic selected from pyrazolyl, thiazolyl,oxazolyl, imidazolyl, isoxazolyl, isothiazolyl, thiadiazolyl,oxadiazolyl, and 1,2,4-triazolyl (in some embodiments, Ar/Het is otherthan 1,2,4-triazolyl and/or furanyl), e.g., Ar/Het is pyrazolyl. Inembodiments, each of R4 and R5 is hydrogen; and/or one or more of thefollowing: (i) R2 is a substituent other than hydrogen (e.g., phenyl,substituted phenyl, thienyl, thiazolyl, and pyrazol-1-yl), and R3 ishydrogen, in certain embodiments, the compounds can exhibit selectivityfor HDAC 1 and/or 2; (ii) R2 is hydrogen, and R3 is a substituent otherthan hydrogen (e.g., fluoro), in certain embodiments, the compounds canexhibit selectivity for HDAC 3; and (iii) each of R2 and R3 is hydrogen.

In certain embodiments, n is 1, and X is—Y—[C(R^(a))₂]_(a)-A-[C(R^(b))₂]_(b)—B—, and Y is O or NR^(e) (e.g., Yis O). Embodiments can include any one or more of the features describedherein. For example, one or both of the following: R1 is C6-C10 aryl(e.g., phenyl), which is optionally substituted with from 1-3 R^(o); andAr/Het is 5 membered heteroaromatic selected from pyrazolyl, thiazolyl,oxazolyl, imidazolyl, isoxazolyl, isothiazolyl, thiadiazolyl,oxadiazolyl, and 1,2,4-triazolyl (in some embodiments, Ar/Het is otherthan 1,2,4-triazolyl and/or furanyl), e.g., Ar/Het is pyrazolyl. Inembodiments, each of R4 and R5 is hydrogen; and/or one or more of thefollowing: (i) R2 is a substituent other than hydrogen (e.g., phenyl,substituted phenyl, thienyl, thiazolyl, and pyrazol-1-yl), and R3 ishydrogen, in certain embodiments, the compounds can exhibit selectivityfor HDAC 1 and/or 2; (ii) R2 is hydrogen, and R3 is a substituent otherthan hydrogen (e.g., fluoro), in certain embodiments, the compounds canexhibit selectivity for HDAC 3; and (iii) each of R2 and R3 is hydrogen.

In certain embodiments, n is 1, and Ar/Het is a bicyclic 8-, 9-, or10-membered azabridged heteroaromatic such as indolizinyl,pyrrolopyrimidinyl, pyrazolopyridinyl, imidazopyridinyl,imidazopyridazinyl, triazolopyridinyl, imidazothiazolyl,imidazooxazolyl, 1,2,4-triazolothiazolyl, and 1,2,4-triazolooxazolyl.Embodiments can include any one or more of the features describedherein. For example, X is a bond and R1 is H. In embodiments, each of R4and R5 is hydrogen; and/or one or more of the following: (i) R2 is asubstituent other than hydrogen (e.g., phenyl, substituted phenyl,thienyl, thiazolyl, and pyrazol-1-yl), and R3 is hydrogen, in certainembodiments, the compounds can exhibit selectivity for HDAC 1 and/or 2;(ii) R2 is hydrogen, and R3 is a substituent other than hydrogen (e.g.,fluoro), in certain embodiments, the compounds can exhibit selectivityfor HDAC 3; and (iii) each of R2 and R3 is hydrogen.

In certain embodiments, n is 0, and U is ═CR^(r) (e.g., R^(r) ishydrogen). Embodiments can include any one or more of the featuresdescribed herein. For example, one or both of the following: Ar′/Het′ isphenyl, which is optionally substituted with from 1-3 R^(p); and havingthe provisions described elsewhere; Cy is a heterocyclyl (e.g., aheterocyclyl that contains a secondary amine as part of its structure).In embodiments, one or more of the following apply: (i) R2 is asubstituent other than hydrogen (e.g., phenyl, substituted phenyl,thienyl, thiazolyl, and pyrazol-1-yl), and R3 is hydrogen, in certainembodiments, the compounds can exhibit selectivity for HDAC 1 and/or 2;(ii) R2 is hydrogen, and R3 is a substituent other than hydrogen (e.g.,fluoro), in certain embodiments, the compounds can exhibit selectivityfor HDAC 3; and (iii) each of R2 and R3 is hydrogen.

Definitions

The term “hepatocyte” refers to commercially available preparations ofliver tissue derived cells that can be obtained from mouse, rat, dog,monkey, or human liver tissue.

The term “mammal” includes organisms, which include mice, rats, cows,sheep, pigs, rabbits, goats, horses, monkeys, dogs, cats, and humans.

“An effective amount” refers to an amount of a compound that confers atherapeutic effect (e.g., treats, e.g., controls, relieves, ameliorates,alleviates, or slows the progression of; or prevents, e.g., delays theonset of or reduces the risk of developing, a disease, disorder, orcondition or symptoms thereof) on the treated subject. The therapeuticeffect may be objective (i.e., measurable by some test or marker) orsubjective (i.e., subject gives an indication of or feels an effect). Aneffective amount of the compound described above may range from about0.01 mg/kg to about 1000 mg/kg, (e.g., from about 0.1 mg/kg to about 100mg/kg, from about 1 mg/kg to about 100 mg/kg). Effective doses will alsovary depending on route of administration, as well as the possibility ofco-usage with other agents.

The term “halo” or “halogen” refers to any radical of fluorine,chlorine, bromine or iodine.

In general, and unless otherwise indicated, substituent (radical) prefixnames are derived from the parent hydride by either (i) replacing the“ane” in the parent hydride with the suffix “yl;” or (ii) replacing the“e” in the parent hydride with the suffix “yl;” (here the atom(s) withthe free valence, when specified, is (are) given numbers as low as isconsistent with any established numbering of the parent hydride).Accepted contracted names, e.g., furyl, pyridyl, and piperidyl, andtrivial names, e.g., phenyl and thienyl are also used herein throughout.Conventional numbering/lettering systems are also adhered to forsubstituent numbering.

The following definitions are used, unless otherwise described. Specificand general values listed below for radicals, substituents, and ranges,are for illustration only; they do not exclude other defined values orother values within defined ranges for the radicals and substituents.Alkyl, alkoxy, and the like denote both straight and branched groups.

As used herein, the term “alkyl,” employed alone or in combination withother terms, refers to a saturated hydrocarbon group that may bestraight-chain or branched. In some embodiments, the alkyl groupcontains 1 to 12, 1 to 8, or 1 to 6 carbon atoms. Examples of alkylmoieties include, but are not limited to, chemical groups such asmethyl, ethyl, n-propyl, isopropyl, n-butyl, tert-butyl, isobutyl,sec-butyl; higher homologs such as 2-methyl-1-butyl, n-pentyl, 3-pentyl,n-hexyl, 1,2,2-trimethylpropyl, n-heptyl, n-octyl, and the like. In someembodiments, the alkyl moiety is methyl, ethyl, n-propyl, isopropyl,n-butyl, isobutyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl,or 2,4,4-trimethylpentyl.

Throughout the definitions, the term “Cy-Cz” (e.g., C1-C6 and the like)is used, wherein y and z are integers and indicate the number ofcarbons, wherein y-z indicates a range which includes the endpoints.

As referred to herein, the term “alkoxy group” refers to a group offormula —O(alkyl). Alkoxy can be, for example, methoxy, ethoxy, propoxy,isopropoxy, butoxy, iso-butoxy, sec-butoxy, pentoxy, 2-pentoxy,3-pentoxy, or hexyloxy.

As used herein, the term “aryl,” employed alone or in combination withother terms, refers to a monocyclic aromatic hydrocarbon moiety or apolycyclic hydrocarbon moiety (e.g., having 2, 3 or 4 fused linkedrings) that includes at least one aromatic ring. Examples include, butare not limited to, phenyl, 1-naphthyl, 2-naphthyl, indanyl andtetralinyl. In some embodiments, aryl groups have from 6 to 10 carbonatoms.

As referred to herein, “heteroaryl” refers to an aromatic monocyclic orfused bicyclic ring that includes at least one aromatic ring, each ofwhich containing at least one (typically one to about three) nitrogen,oxygen, or sulfur ring atoms (independently selected when more than oneis present). Examples of heteroaryl groups include, but are not limitedto pyridyl, pyrazolyl, pyrrolyl, 2-oxo-indolyl, quinolinyl,isoquinolinyl, tetrahydro-isoquinolinyl, benzofuranyl, indolyl,benzodioxanyl, benzodioxolyl (aka. methylenedioxyphenyl) andcorresponding difluoro (CF₂) analog, thiazolyl, 2-oxopyridinyl,pyridinyl N-oxide, pyrimidinyl, thienyl, furanyl, oxazolyl, isoxazolyl,pyridazinyl, imidazolyl, pyrazinyl, isothiazolyl,1,2-thiazinyl-1,1-dioxide, benzimidazolyl, thiadiazolyl, benzopyranyl,benzothiazolyl, benzotriazolyl, benzoxazolyl, benzothienyl, oxadiazolyl,triazolyl, tetrazolyl, dioxoindolyl (isatin), phthalimido; heteroarylsthat contain a bridgehead nitrogen ring atom and optionally otherheteroatom ring atoms, such as indolizinyl, pyrrolopyrimidinyl,pyrazolopyridinyl, imidazopyridinyl, imidazopyriazinyl,triazolopyridinyl, imidazothiazolyl, imidazooxazolyl); and the dihydroand tetrahydro congeners of the fully unsaturated ring systems.

As used herein, the phrase “optionally substituted” means unsubstituted(e.g., substituted with a H) or substituted. As used herein, the term“substituted” means that a hydrogen atom is removed and replaced by asubstitutent. It is understood that substitution at a given atom islimited by valency. The use of a substituent (radical) prefix name suchas alkyl without the modifier “optionally substituted” or “substituted”is understood to mean that the particular substituent is unsubstituted.However, the use of “fluoro Cy-Cz alkyl” without the modifier“optionally substituted” or “substituted” is still understood to mean analkyl group, in which at least one hydrogen atom is replaced by fluoro.

Unless indicated otherwise, the nomenclature of substituents that arenot explicitly defined herein are arrived at by naming the terminalportion of the functionality followed by the adjacent functionalitytoward the point of attachment. In generally, the point of attachmentfor a substituent is indicated by the last term in the group. Forexample, (heterocyclyl)-(C1-C6) alkyl refers to a moiety ofheteroaryl-alkylene-, wherein the alkylene linker has 1 to 6 carbons,and the substituent is attached through the alkylene linker.

As used herein, the term “cycloalkyl,” employed alone or in combinationwith other terms, refers to a saturated, cyclic hydrocarbon moiety.Exemplary cycloalkyl groups include, without limitation, cyclopropyl,cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.

As used herein, the term “cyano,” employed alone or in combination withother terms, refers to a group of formula —CN, wherein the carbon andnitrogen atoms are bound together by a triple bond.

As used herein, the term “halo Cy-Cz alkyl” and the like employed aloneor in combination with other terms, refers to an alkyl group having fromone halogen atom to 2n+1 halogen atoms which may be the same ordifferent, where “n” is the number of carbon atoms in the alkyl group.In some embodiments, the halogen atoms are fluoro atoms.

As used herein, “haloalkoxy,” employed alone or in combination withother terms, refers to a group of formula —O-haloalkyl. An examplehaloalkoxy group is OCF₃. In some embodiments, the halogen atoms arefluoro atoms.

As used herein, the term “heterocyclyl” employed alone or in combinationwith other terms, refers to a saturated ring system, which has carbonring atoms and at least one heteroatom ring atom selected from nitrogen,sulfur, and oxygen (independently selected when more than one ispresent). When the heterocyclyl group contains more than one heteroatom,the heteroatoms may be the same or different. Heterocyclyl groups caninclude mono- or bicyclic (e.g., having 2 fused rings) ring systems.Heterocyclyl groups can also include bridgehead heterocycloalkyl groups.As used herein, “bridgehead heterocyclyl group” refers to a heterocyclylmoiety containing at least one bridgehead heteroatom (e.g., nitrogen).In some embodiments, the carbon atoms or hetereoatoms in the ring(s) ofthe heterocycloalkyl group can be oxidized to form a carbonyl, orsulfonyl group (or other oxidized linkage) or a nitrogen atom can bequaternized.

As to any of the above groups that contain one or more substituents, itis understood, of course, that such groups do not contain anysubstitution or substitution patterns that are sterically impracticaland/or synthetically unfeasible. In addition, the compounds of thisinvention include all stereochemical isomers arising from thesubstitution of these compounds.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Other features and advantages of the invention will be apparent from thefollowing detailed description, and from the claims.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, can also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention which are, for brevity, described in thecontext of a single embodiment, can also be provided separately or inany suitable sub-combination.

Thus, for ease of exposition, it is also understood that where in thisspecification, a group is defined by “as defined anywhere herein” (orthe like), the definitions for that particular group include the firstoccurring and broadest generic definition as well as any sub-generic andspecific definitions delineated anywhere in this specification. Also,for ease of exposition, the definition “substituent other than hydrogen”refers collectively to the non-hydrogen possibilities for thatparticular variable.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGURE is a bar graph shows the effect of compounds on long-term memoryfor object recognition. The data is presented as discrimination indexbetween known and novel object as a function of compound and dose. Inthe leftmost cluster of bars, the dosages represented from left to rightare (0, 3, 10, 30 mg/kg); in the center and rightmost cluster of bars,the dosages represented from left to right are (3, 10, 30 mg/kg).

DETAILED DESCRIPTION

Compounds of formula (I) described herein may contain one or moreasymmetric centers and thus occur as racemates and racemic mixtures,single enantiomers, individual diastereomers and diastereomericmixtures. While shown without respect to the stereochemistry in formula(I), the present invention includes such optical isomers (enantiomers)and diastereomers; as well as the racemic and resolved, enantiomericallypure R and S stereoisomers; as well as other mixtures of the R and Sstereoisomers and pharmaceutically acceptable salts thereof. The use ofthese compounds is intended to cover the racemic mixture or either ofthe chiral enantiomers.

Compounds of formula (I) described herein may also contain linkages(e.g., carbon-carbon bonds, carbon-nitrogen bonds such as amide bonds)wherein bond rotation is restricted about that particular linkage, e.g.restriction resulting from the presence of a ring or double bond.Accordingly, all cis/trans and E/Z isomers and rotational isomers areexpressly included in the present invention.

One skilled in the art will also recognize that it is possible fortautomers to exist for the compounds described herein. The inventionincludes all such tautomers even though not shown in the formulasherein. All such isomeric forms of such compounds are expressly includedin the present invention.

Optical isomers can be obtained in pure form by standard proceduresknown to those skilled in the art, and include, but are not limited to,diastereomeric salt formation, kinetic resolution, and asymmetricsynthesis. See, for example, Jacques, et al., Enantiomers, Racemates andResolutions (Wiley Interscience, New York, 1981); Wilen, S. H., et al.,Tetrahedron 33:2725 (1977); Eliel, E. L. Stereochemistry of CarbonCompounds (McGraw-Hill, N Y, 1962); Wilen, S. H. Tables of ResolvingAgents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of NotreDame Press, Notre Dame, Ind. 1972), each of which is incorporated hereinby reference in their entireties. It is also understood that thisinvention encompasses all possible regioisomers, and mixtures thereof,which can be obtained in pure form by standard separation proceduresknown to those skilled in the art, and include, but are not limited to,column chromatography, thin-layer chromatography, and high-performanceliquid chromatography.

The compounds described herein also include the various hydrate andsolvate forms of the compounds.

Compounds described herein can also include all isotopes of atomsoccurring in the intermediates or final compounds. Isotopes includethose atoms having the same atomic number but different mass numbers.For example, isotopes of hydrogen include tritium and deuterium.

The compounds described herein also include pharmaceutically acceptablesalts of the compounds disclosed herein. As used herein, the term“pharmaceutically acceptable salt” refers to a salt formed by theaddition of a pharmaceutically acceptable acid or base to a compounddisclosed herein. As used herein, the phrase “pharmaceuticallyacceptable” refers to a substance that is acceptable for use inpharmaceutical applications from a toxicological perspective and doesnot adversely interact with the active ingredient. Pharmaceuticallyacceptable salts, including mono- and bi-salts, include, but are notlimited to, those derived from organic and inorganic acids such as, butnot limited to, acetic, lactic, citric, cinnamic, tartaric, succinic,fumaric, maleic, malonic, mandelic, malic, oxalic, propionic,hydrochloric, hydrobromic, phosphoric, nitric, sulfuric, glycolic,pyruvic, methanesulfonic, ethanesulfonic, toluenesulfonic, salicylic,benzoic, and similarly known acceptable acids. Lists of suitable saltsare found in Remington's Pharmaceutical Sciences, 17th ed., MackPublishing Company, Easton, Pa., 1985, p. 1418; Journal ofPharmaceutical Science, 66, 2 (1977); and “Pharmaceutical Salts:Properties, Selection, and Use A Handbook; Wermuth, C. G. and Stahl, P.H. (eds.) Verlag Helvetica Chimica Acta, Zurich, 2002 [ISBN3-906390-26-8] each of which is incorporated herein by reference intheir entireties.

In some embodiments, the compounds are prodrugs. As used herein,“prodrug” refers to a moiety that releases a compound described hereinwhen administered to a patient. Prodrugs can be prepared by modifyingfunctional groups present in the compounds in such a way that themodifications are cleaved, either in routine manipulation or in vivo, tothe parent compounds. Examples of prodrugs include compounds asdescribed herein that contain one or more molecular moieties appended toa hydroxyl, amino, sulfhydryl, or carboxyl group of the compound, andthat when administered to a patient, cleave in vivo to form the freehydroxyl, amino, sulfhydryl, or carboxyl group, respectively. Examplesof prodrugs include, but are not limited to, acetate, formate andbenzoate derivatives of alcohol and amine functional groups in thecompounds described herein. Preparation and use of prodrugs is discussedin T. Higuchi and V. Stella, “Pro-drugs as Novel Delivery Systems,” Vol.14 of the A.C.S. Symposium Series, and in Bioreversible Carriers in DrugDesign, ed. Edward B. Roche, American Pharmaceutical Association andPergamon Press, 1987, both of which are incorporated herein by referencein their entireties.

Synthesis of Compounds of Formula (I)

The compounds described herein can be prepared in a variety of waysknown to one skilled in the art of organic synthesis. The compoundsdescribed herein can be synthesized using the methods as hereinafterdescribed below, together with synthetic methods known in the art ofsynthetic organic chemistry or variations thereon as appreciated bythose skilled in the art.

Compounds of the present invention can be conveniently prepared inaccordance with the procedures outlined in the Examples section, fromcommercially available starting materials, compounds known in theliterature, or readily prepared intermediates, by employing conventionalsynthetic methods and procedures known to those skilled in the art.Conventional synthetic methods and procedures for the preparation oforganic molecules and functional group transformations and manipulationscan be readily obtained from the relevant scientific literature or fromstandard textbooks in the field. It will be appreciated that, wheretypical or preferred process conditions (i.e., reaction temperatures,times, mole ratios of reactants, solvents, pressures, etc.) are given,other process conditions can also be used unless otherwise stated.Optimum reaction conditions may vary with the particular reactants orsolvent used, but such conditions can be determined by one skilled inthe art by routine optimization procedures. Those skilled in the art oforganic synthesis will recognize that the nature and order of thesynthetic steps presented may be varied for the purpose of optimizingthe formation of the compounds described herein.

Synthetic chemistry transformations useful in synthesizing the compoundsdescribed herein are known in the art and include, for example, thosesuch as described in R. C. Larock, Comprehensive OrganicTransformations, 2d.ed., Wiley-VCH Publishers (1999); P. G. M. Wuts andT. W. Greene, Protective Groups in Organic Synthesis, 4th Ed., JohnWiley and Sons (2007); L. Fieser and M. Fieser, Fieser and Fieser'sReagents for Organic Synthesis, John Wiley and Sons (1994); and L.Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, JohnWiley and Sons (1995), and subsequent editions thereof. Preparation ofcompounds can involve the protection and deprotection of variouschemical groups. The need for protection and deprotection, and theselection of appropriate protecting groups can be readily determined byone skilled in the art. The chemistry of protecting groups can be found,for example, in Wuts P G M and Greene T W, 2006, Greene's ProtectiveGroups in Organic Synthesis, Fourth Edition, John Wiley & Sons, Inc.,Hoboken, N.J., USA, which is incorporated herein by reference in itsentirety. Adjustments to the protecting groups and formation andcleavage methods described herein may be adjusted as necessary in lightof the various substituents.

The reactions of the processes described herein can be carried out insuitable solvents which can be readily selected by one of skill in theart of organic synthesis. Suitable solvents can be substantiallynonreactive with the starting materials (reactants), the intermediates,or products at the temperatures at which the reactions are carried out,i.e., temperatures which can range from the solvent freezing temperatureto the solvent boiling temperature. A given reaction can be carried outin one solvent or a mixture of more than one solvent. Depending on theparticular reaction step, suitable solvents for a particular reactionstep can be selected.

The processes described herein can be monitored according to anysuitable method known in the art. For example, product formation can bemonitored by spectroscopic means, such as nuclear magnetic resonancespectroscopy (e.g., ¹H and/or ¹³C NMR) infrared spectroscopy,spectrophotometry (e.g., UV-visible), or mass spectrometry, or bychromatography such as high performance liquid chromatography (HPLC) orthin layer chromatography.

The compounds described herein can be separated from a reaction mixtureand further purified by a method such as column chromatography,high-performance liquid chromatography (HPLC), or recrystallization.

One of skill in the art will recognize that there are additional methodsof producing the compounds of formula (I) in addition to those describedin the Examples section.

Use

A histone deacetylase (HDAC), as described herein, can be anypolypeptide having features characteristic of polypeptides that catalyzethe removal of the acetyl group (deacetylation) from acetylated targetproteins. Features characteristic of HDACs are known in the art (see,for example, Finnin et al., 1999, Nature, 401:188). Thus, an HDAC can bea polypeptide that represses gene transcription by deacetylating theε-amino groups of conserved lysine residues located at the N-termini ofhistones, e.g., H3, H4, H2A, and H2B, which form the nucleosome. HDACsalso deacetylate other proteins such as p53, E2F, α-tubulin, and MyoD(see, for example, Annemieke et al., 2003, Biochem. J., 370:737). HDACscan also be localized to the nucleus and certain HDACs can be found inboth the nucleus and also the cytoplasm.

Compounds of formula (I) described herein may interact with any HDAC. Insome embodiments, the compounds of formula (I) described herein willhave at least about 2-fold (e.g., at least about 5-fold, 10-fold,15-fold, or 20-fold) greater activity to inhibit one or more class IHDACS (e.g., HDAC1, HDAC2, or HDAC3) as compared to one or more otherHDACs (e.g., one or more HDACs of class Ha, IIb, or IV).

The invention features a method of treating a cancer in patient in needthereof, comprising administering a therapeutically effective amount ofan HDAC inhibitor as described herein, or pharmaceutically, acceptablesalt thereof. In some embodiments, the cancer is a solid tumor,neoplasm, carcinoma, sarcoma, leukemia, or lymphoma. In someembodiments, leukemias include acute leukemias and chronic leukemiassuch as acute lymphocytic leukemia (ALL), acute myeloid leukemia,chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML)and Hairy Cell Leukemia; lymphomas such as cutaneous T-cell lymphomas(CTCL), noncutaneous peripheral T-cell lymphomas, lymphomas associatedwith human T-cell lymphotrophic virus (fITLV) such as adult T-cellleukemia/lymphoma (ATLL), Hodgkin's disease and non-Hodgkin's lymphomas,large-cell lymphomas, diffuse large B-cell lymphoma (DLBCL); Burkitt'slymphoma; primary central nervous system (CNS) lymphoma; multiplemyeloma; childhood solid tumors such as brain tumors, neuroblastoma,retinoblastoma, Wilm's tumor, bone tumors, and soft-tissue sarcomas,common solid tumors of adults such as head and neck cancers (e.g., oral,laryngeal and esophageal), genitor-urinary cancers (e.g., prostate,bladder, renal, uterine, ovarian, testicular, rectal and colon), lungcancer, breast cancer.

In some embodiments, the cancer is (a) Cardiac: sarcoma (angiosarcoma,fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyoma,fibroma, lipoma and teratoma; (b) Lung: bronchogenic carcinoma (squamouscell, undifferentiated small cell, undifferentiated large cell,adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchial adenoma,sarcoma, lymphoma, chondromatous hamartoma, mesothelioma; (c)Gastrointestinal: esophagus (squamous cell carcinoma, adenocarcinoma,leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma,leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma,glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel(adenocarcinoma, lymphoma, carcinoid tumors, Karposi's sarcoma,leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel(adenocarcinoma, tubular adenoma, villous adenoma, hamartoma,leiomyoma); (d) Genitourinary tract: kidney (adenocarcinoma, Wilm'stumor (nephroblastoma), lymphoma, leukemia), bladder and urethra(squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma),prostate (adenocarcinoma, sarcoma), testis (seminoma, teratoma,embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma,interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors,lipoma); (e) Liver: hepatoma (hepatocellular carcinoma),cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellularadenoma, hemangioma; (f) Bone: osteogenic sarcoma (osteosarcoma),fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing'ssarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma,malignant giant cell tumor chordoma, osteochrondroma (osteocartilaginousexostoses), benign chondroma, chondroblastoma, chondromyxofibroma,osteoid osteoma and giant cell tumors; (g) Nervous system: skull(osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meninges(meningioma, meningiosarcoma, gliomatosis), brain (astrocytoma,medulloblastoma, glioma, ependymoma, germinoma (pinealoma), glioblastomamultiform, oligodendroglioma, schwannoma, retinoblastoma, congenitaltumors), spinal cord (neurofibroma, meningioma, glioma, sarcoma); (h)Gynecological: uterus (endometrial carcinoma), cervix (cervicalcarcinoma, pre-tumor cervical dysplasia), ovaries (ovarian carcinoma,serous cystadenocarcinoma, mucinous cystadenocarcinoma), unclassifiedcarcinoma (granulosa-thecal cell tumors, Sertoli-Leydig cell tumors,dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma,intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma),vagina (clear cell carcinoma, squamous cell carcinoma, botryoidsarcoma), embryonal rhabdomyosarcoma, fallopian tubes (carcinoma); (i)Hematologic: blood (myeloid leukemia [acute and chronic], acutelymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferativediseases, multiple myeloma, myelodysplastic syndrome), Hodgkin'sdisease, non-Hodgkin's lymphoma (malignant lymphoma); (j) Skin:malignant melanoma, basal cell carcinoma, squamous cell carcinoma,Karposi's sarcoma, moles dysplastic nevi, lipoma, angioma,dermatofibroma, keloids, psoriasis; and (k) Adrenal glands:neuroblastoma conditions.

In another aspect, the present invention provides a method of treating ainflammatory disorder in patient in need thereof, comprisingadministering a therapeutically effective amount of a compound offormula (I) as described herein, or pharmaceutically, acceptable saltthereof. In some embodiments, the inflammatory disorder is an acute andchronic inflammatory disease, autoimmune disease, allergic disease,disease associated with oxidative stress, and diseases characterized bycellular hyperproliferation. Non-limiting examples are inflammatoryconditions of a joint including rheumatoid arthritis (RA) and psoriaticarthritis; inflammatory bowel diseases such as Crohn's disease andulcerative colitis; spondyloarthropathies; scleroderma; psoriasis(including T-cell mediated psoriasis) and inflammatory dermatoses suchan dermatitis, eczema, atopic dermatitis, allergic contact dermatitis,urticaria; vasculitis (e.g., necrotizing, cutaneous, andhypersensitivity vasculitis); eosinophilic myositis, eosinophilicfasciitis; cancers with leukocyte infiltration of the skin or organs,ischemic injury, including cerebral ischemia (e.g., brain injury as aresult of trauma, epilepsy, hemorrhage or stroke, each of which may leadto neurodegeneration); HIV, heart failure, chronic, acute or malignantliver disease, autoimmune thyroiditis; systemic lupus erythematosus,Sjorgren's syndrome, lung diseases (e.g., ARDS); acute pancreatitis;amyotrophic lateral sclerosis (ALS); Alzheimer's disease;cachexia/anorexia; asthma; atherosclerosis; chronic fatigue syndrome,fever; diabetes (e.g., insulin diabetes or juvenile onset diabetes);glomerulonephritis; graft versus host rejection (e.g., intransplantation); hemorrhagic shock; hyperalgesia: inflammatory boweldisease; multiple sclerosis; myopathies (e.g., muscle proteinmetabolism, esp. in sepsis); osteoarthritis; osteoporosis; Parkinson'sdisease; pain; pre-term labor; psoriasis; reperfusion injury;cytokine-induced toxicity (e.g., septic shock, endotoxic shock); sideeffects from radiation therapy, temporal mandibular joint disease, tumormetastasis; or an inflammatory condition resulting from strain, sprain,cartilage damage, trauma such as burn, orthopedic surgery, infection orother disease processes.

Allergic diseases and conditions, include but are not limited torespiratory allergic diseases such as asthma, allergic rhinitis,hypersensitivity lung diseases, hypersensitivity pneumonitis,eosinophilic pneumonias (e.g., Loeffler's syndrome, chronic eosinophilicpneumonia), delayed-type hypersensitivity, interstitial lung diseases(ILD) (e.g., idiopathic pulmonary fibrosis, or ILD associated withrheumatoid arthritis, systemic lupus erythematosus, ankylosingspondylitis, systemic sclerosis, Sjogren's syndrome, polymyositis ordermatomyositis); systemic anaphylaxis or hypersensitivity responses,drug allergies (e.g., to penicillin, cephalosporins), insect stingallergies, and the like.

In another aspect, the present invention provides a method of preventingor treating a memory-related disorder in patient in need thereof,comprising administering a therapeutically effective amount of acompound of formula (I) as described herein, or pharmaceutically,acceptable salt thereof. Compounds of formula (I) can be used to treatpatients with memory impairments associated with direct cognitivedisorders such as amnesia, dementia and delirium; anxiety disorders suchas phobias, panic disorders, psychosocial stress (e.g. as seen indisaster, catastrophe or violence victims), obsessive-compulsivedisorder, generalized anxiety disorder and post-traumatic stressdisorder; mood disorders such as depression and bipolar disorder; andpsychotic disorders such as schizophrenia and delusional disorder.Memory impairment, a hallmark of neurodegenerative diseases such as, butnot limited to, Parkinson's, Alzheimer's, Huntington's, amyotrophiclateral sclerosis (ALS), spinocerebellar ataxia, as well as aging, canalso be treated by using compounds of formula (I). In addition,compounds of the invention can be used to treat drug addiction throughextinction of drug-seeking behavior.

In a further aspect, this application features methods of treating aneurological condition (e.g., Friedreich's ataxia (FRDA), myotonicdystrophy, spinal muscular atrophy, fragile X syndrome, Huntington'sdisease, a spinocerebellar ataxia, Kennedy's disease, amyotrophiclateral sclerosis, Niemann Pick, Pitt Hopkins, spinal and bulbarmuscular atrophy, Alzheimer's disease or schizophrenia, bipolardisorder, and related diseases) that include administering a compound offormula (I) described herein to a patient having a neurologicalcondition.

In another aspect, this application features the use of a compound offormula (I) described herein in the preparation of a medicament for thetreatment or prevention of a neurological condition (e.g., Friedreich'sataxia, myotonic dystrophy, spinal muscular atrophy, fragile X syndrome,Huntington's disease, a spinocerebellar ataxia, Kennedy's disease,amyotrophic lateral sclerosis, Niemann Pick, Pitt Hopkins, spinal andbulbar muscular atrophy, or Alzheimer's disease); a memory-affectingcondition or disease, a cancer; or an inflammatory disorder, or aPlasmodium falciparum infection (e.g., malaria).

In a further aspect, the application provides a kit for the treatment orprevention of a disorder selected from a neurological disorder (e.g.,Friedreich's ataxia, myotonic dystrophy, spinal muscular atrophy,fragile X syndrome, Huntington's disease, a spinocerebellar ataxia,Kennedy's disease, amyotrophic lateral sclerosis, spinal and bulbarmuscular atrophy, or Alzheimer's disease), a memory-affecting conditionor disease, a cancer, an inflammatory disorder, or a Plasmodiumfalciparum infection (e.g., malaria) in a patient in need thereof,comprising (i) a compound of formula (I) described herein or apharmaceutically acceptable salt thereof; and (ii) instructionscomprising a direction to administer said compound to said patient.

In some embodiments of the above methods, the methods further includeassaying the activity of the candidate compound to increase expressionof one or more genes whose expression is decreased in the neurologicalcondition (e.g., frataxin, huntingtin, brain derived neurotrophic factor(BDNF), peroxisome proliferator-activated receptor-gamma, coactivator 1,alpha (PGC1A), ataxin, fragile X mental retardation (FMR1), dystrophiamyotonica protein kinase (DMPK), or androgen receptor). In someembodiments, the activity of the candidate compound to increaseexpression of one or more genes whose expression is decreased in theneurological condition is measured in an animal, e.g., an animal modelof the neurological condition.

In some embodiments of the above methods, the method is repeated for aplurality of test compounds (e.g., at least 10, 20, 50, 100, 200, 500,or 1000 test compounds).

In another aspect, this application features methods of treating aneurological condition (e.g., Friedreich's ataxia, myotonic dystrophy,spinal muscular atrophy, fragile X syndrome, Huntington's disease,spinocerebellar ataxias, Kennedy's disease, amyotrophic lateralsclerosis, spinal and bulbar muscular atrophy, or Alzheimer's disease)that include performing any of the above methods, formulating thecandidate compound in a pharmaceutical composition, and administeringthe pharmaceutical composition to a patient having a neurologicalcondition.

HDAC inhibitors have been shown to have antimalarial activity (Andrewset al., 2000, Int. J. Parasitol., 30:761-768; Andrews et al.,Antimicrob. Agents Chemother., 52:1454-61). The present inventionprovides methods of treating a Plasmodium falciparum infection (e.g.,malaria) in a patient in need thereof.

HDAC inhibitors may also be useful to treat infectious disease such asviral infections. For example, treatment of HIV infected cells with HDACinhibitors and anti-retroviral drugs can eradicate virus from treatedcells (Blazkova j et al J Infect Dis. 2012 Sep. 1; 206(5):765-9; ArchinN M et al Nature 2012 Jul. 25, 487(7408):482-5). The present inventionsprovides methods of treating a HIV infection in need thereof.

Pharmaceutical Compositions

HDAC inhibitors can be administered neat or formulated as pharmaceuticalcompositions. Pharmaceutical compositions include an appropriate amountof the HDAC inhibitor in combination with an appropriate carrier andoptionally other useful ingredients.

Acceptable salts of the formula (I) compounds described herein include,but are not limited to, those prepared from the following acids: alkyl,alkenyl, aryl, alkylaryl and alkenylaryl mono-, di- and tricarboxylicacids of 1 to 20 carbon atoms, optionally substituted by 1 to 4hydroxyls; alkyl, alkenyl, aryl, alkylaryl and alkenylaryl mono-, di-and trisulfonic acids of 1 to 20 carbon atoms, optionally substituted by1 to 4 hydroxyls; dibasic acids and mineral acids. Examples includehydrochloric; hydrobromic; sulfuric; nitric; phosphoric; lactic(including (+)-L-lactic, (+/−)-DL-lactic); fumaric; glutaric; maleic;acetic; salicyclic; p-toluenesulfonic; tartaric (including(+)-L-tartaric); citric; methanesulfonic; formic; malonic; succinic;naphthalene-2-sulfonic; and benzenesulfonic acids. Also,pharmaceutically-acceptable salts can be prepared as amine salts,ammonium salts, or alkaline metal or alkaline earth salts, such assodium, potassium or calcium salts of the carboxylic acid group. Theseare formed from alkaline metal or alkaline earth metal bases or fromamine compounds.

Pharmaceutical compositions of formula (I) compounds described hereinsuitable for oral administration can be in the form of (1) discreteunits such as capsules, sachets, tablets, or lozenges each containing apredetermined amount of the HDAC inhibitor; (2) a powder or granules;(3) a bolus, electuary, or paste; (4) a solution or a suspension in anaqueous liquid or a non-aqueous liquid; or (5) an oil-in-water liquidemulsion or a water-in-oil liquid emulsion. Compositions suitable fortopical administration in the mouth, for example buccally orsublingually, include lozenges. Compositions suitable for parenteraladministration include aqueous and non-aqueous sterile suspensions orinjection solutions. Compositions suitable for rectal administration canbe presented as a suppository.

Pharmaceutical compositions of formula (I) compounds described hereincan be formulated using a solid or liquid carrier. The solid or liquidcarrier should be compatible with the other ingredients of theformulation and not deleterious to the recipient. If the pharmaceuticalcomposition is in tablet form, then the HDAC inhibitor is mixed with acarrier having the necessary compression properties in suitableproportions and compacted in the shape and size desired. If thecomposition is in powder form, the carrier is a finely divided solid inadmixture with the finely divided active ingredient. The powders andtablets can contain up to 99% of the active ingredient. Suitable solidcarriers include, for example, calcium phosphate, magnesium stearate,talc, sugars, lactose, dextrin, starch, gelatin, cellulose, methylcellulose, sodium carboxymethyl cellulose, polyvinylpyrrolidine, lowmelting waxes and ion exchange resins. A solid carrier can include oneor more substances that can act as flavoring agents, lubricants,solubilizers, suspending agents, fillers, glidants, compression aids,binders or tablet-disintegrating agents. A suitable carrier can also bean encapsulating material.

If the composition is a solution, suspension, emulsion, syrup, elixir,or pressurized composition, then liquid carriers can be used. In thiscase, the HDAC inhibitor is dissolved or suspended in a pharmaceuticallyacceptable liquid carrier. Suitable examples of liquid carriers for oraland parenteral administration include (1) water; (2) alcohols, e.g.monohydric alcohols and polyhydric alcohols such as glycols, and theirderivatives; and (3) oils, e.g. fractionated coconut oil and arachisoil. For parenteral administration, the carrier can also be an oilyester such as ethyl oleate and isopropyl myristate. Liquid carriers forpressurized compositions include halogenated hydrocarbon or otherpharmaceutically acceptable propellants. The liquid carrier can containother suitable pharmaceutical additives such as solubilizers;emulsifiers; buffers; preservatives; sweeteners; flavoring agents;suspending agents; thickening agents; colors; viscosity regulators;stabilizers; osmo-regulators; cellulose derivatives such as sodiumcarboxymethyl cellulose; antioxidants; and bacteriostatics. Othercarriers include those used for formulating lozenges such as sucrose,acacia, tragacanth, gelatin and glycerin as well as those used informulating suppositories such as cocoa butter or polyethylene glycol.

If the composition is to be administered intravenously orintraperitoneally by infusion or injection, solutions of the HDACinhibitor can be prepared in water, optionally mixed with a nontoxicsurfactant. Dispersions can also be prepared in glycerol, liquidpolyethylene glycols, triacetin, and mixtures thereof and in oils. Underordinary conditions of storage and use, these preparations contain apreservative to prevent the growth of microorganisms. The compositionsuitable for injection or infusion can include sterile aqueous solutionsor dispersions or sterile powders comprising the active ingredient,which are adapted for the extemporaneous preparation of sterileinjectable or infusible solutions or dispersions, optionallyencapsulated in liposomes. In all cases, the ultimate dosage form shouldbe sterile, fluid and stable under the conditions of manufacture andstorage. The liquid carrier or vehicle can be a solvent or liquiddispersion medium as described above. The proper fluidity can bemaintained, for example, by the formation of liposomes, by themaintenance of the required particle size in the case of dispersions orby the use of surfactants. The prevention of the action ofmicroorganisms can be brought about by various antibacterial andantifungal agents, for example, parabens, chlorobutanol, phenol, sorbicacid, thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars, buffers or sodiumchloride. Prolonged absorption of the injectable compositions can bebrought about by the use in the compositions of agents delayingabsorption, for example, aluminum monostearate and gelatin. Sterileinjectable solutions are prepared by incorporating the HDAC inhibitor inthe required amount in the appropriate solvent with some of the otheringredients enumerated above, as required, followed by filtersterilization. In the case of sterile powders for the preparation ofsterile injectable solutions, the preferred methods of preparation arevacuum drying and the freeze-drying techniques, which yield a powder ofthe HDAC inhibitor, plus any additional desired ingredient present inthe previously sterile-filtered solutions.

Pharmaceutical compositions can be in unit-dose or multi-dose form or ina form that allows for slow or controlled release of the HDAC inhibitor.Each unit-dose can be in the form of a tablet, capsule or packagedcomposition such as, for example, a packeted powder, vial, ampoule,prefilled syringe or sachet containing liquids. The unit-dose form alsocan be the appropriate number of any such compositions in package form.Pharmaceutical compositions in multi-dose form can be packaged incontainers such as sealed ampoules and vials. In this case, the HDACinhibitor can be stored in a freeze-dried (lyophilized) conditionrequiring only the addition of a sterile liquid carrier immediatelyprior to use. In addition, extemporaneous injection solutions andsuspensions can be prepared from sterile powders, granules and tabletsof the kind previously described.

EXAMPLES

Method A

Compounds described herein, where n=1, and where R1, X, Ar/Het, R2, R3,R4, R5 are defined as described anywhere herein, can be obtained byreaction of a mono- or bicyclic heterocycle aldehyde or ketone,synthesized using methods well known by those skilled in the art (seefor example Joule J A and Mills K, Heterocyclic Chemistry, FifthEdition, John Wiley & Sons, Inc., Hoboken, N.J., USA) with a Wittig orHomer-Wadsworth-Emmons reagent to form a γ-substituted acrylate ester.After saponification, a substituted or unsubstitutedN-(o-aminophenyl)amide is prepared by an amide-forming reaction of theacrylic acid with a protected or unprotected substituted orunsubstituted o-phenylenediamine, where P is a protecting group asdefined in Wuts P G M and Greene T W, 2006, Greene's Protective Groupsin Organic Synthesis, Fourth Edition, John Wiley & Sons, Inc., Hoboken,N.J., USA. Compounds of the invention can be obtained after deprotectionif required using methods well known to those skilled in the art andwhich are described for example in Wuts P G M and Greene T W, 2006,Greene's Protective Groups in Organic Synthesis, Fourth Edition, JohnWiley & Sons, Inc., Hoboken, N.J., USA.

Example 1: hydrochloride salt of(E)-N-(2-aminophenyl)-3-(imidazo[1,2-a]pyridin-3-yl)acrylamide A6

(E)-ethyl 3-(imidazo[1,2-a]pyridin-3-yl)acrylate

(Ethoxycarbonylmethylene)triphenylphosphorane (0.72 g, 2.05 mmol) wasadded to a solution of imidazo[1,2-a]pyridine-3-carbaldehyde (0.25 g,1.71 mmol) in anhydrous tetrahydrofuran (THF) (20 mL) at roomtemperature. The reaction mixture was heated overnight at 65° C. Aftercompletion of the reaction as indicated by HPLC, the reaction mixturewas diluted with ethyl acetate (EtOAc) (20 mL) and quenched with asaturated solution of ammonium chloride (10 mL). The organic layer waswashed with water (3×20 mL) and brine (15 mL). It was dried overanhydrous Na₂SO₄, filtered and evaporated to get the crude product. Thiscrude was purified by silica gel column chromatography using 50-80%EtOAc in Hexanes to provide pure (E)-ethyl3-(imidazo[1,2-a]pyridin-3-yl)acrylate (0.19 g) as a white solid. ES⁺(M+H)⁺ 217.

(E)-3-(imidazo[1,2-a]pyridin-3-yl)acrylic acid

A 1M aqueous solution of KOH (2.2 mL) was added to a solution of(E)-ethyl 3-(imidazo[1,2-a]pyridin-3-yl)acrylate (0.19 g, 0.88 mmol) inEtOH:THF (1:1 v/v) (10 mL). The resulting solution was heated at 50° C.for 3 h. After completion of the reaction the reaction mixture wasevaporated and water (10 mL) was added to the residue. This solution wascarefully acidified to pH 4 with a 3 M HCl aqueous solution. Since theproduct, (E)-3-(imidazo[1,2-a]pyridin-3-yl)acrylic acid, was soluble inwater, the solution was concentrated under reduced pressure and thesolid residue was used directly for the next step. ES⁺ (M+H)⁺ 189.

(E)-tert-butyl(2-(3-(imidazo[1,2-a]pyridin-3-yl)acrylamido)phenyl)carbamate

Diisopropylethylamine (DIPEA, 0.34 g, 2.63 mmol) was added to a solutionof (E)-3-(imidazo[1,2-a]pyridin-3-yl)acrylic acid (0.17 g, 0.88 mmol) in20 mL of dichloromethane (DCM). After addition oftert-butyl-2-aminophenylcarbamate (0.22 g, 1.65 mmol) and2-(1H-7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyluroniumhexafluorophosphate (HATU, 0.43 g, 1.14 mmol) the reaction mixture wasstirred overnight at room temperature under a nitrogen atmosphere. Aftercompletion of the reaction as indicated by HPLC, the reaction mixturewas washed with saturated sodium bicarbonate (NaHCO₃) and brine. It wasdried over Na₂SO₄, filtered and evaporated to give crude (E)-tert-butyl(2-(3-(imidazo[1,2-a]pyridin-3-yl)acrylamido)phenyl)carbamate. The solidwas washed with ethyl acetate (50 mL) and saturated NaHCO₃ gave pureproduct as a light colored solid (0.11 g). ES⁺ (M+H)⁺ 379.

(E)-N-(2-aminophenyl)-3-(imidazo[1,2-a]pyridin-3-yl)acrylamide

A 4 M solution of HCl in dioxane (2.5 mL) was added to a solution of(E)-tert-butyl(2-(3-(imidazo[1,2-a]pyridin-3-yl)acrylamido)phenyl)carbamate (0.11 g,0.29 mmol) in dioxane (2.5 mL). The mixture was stirred at roomtemperature for 3 h. Precipitate formation was observed. Aftercompletion of the reaction as indicated by HPLC/MS, the reaction mixturewas diluted with diethyl ether (20 mL) and the salt was filtered, washedwith ether and dried overnight to get the HCl salt of(E)-N-(2-aminophenyl)-3-(imidazo[1,2-a]pyridin-3-yl)acrylamide (80 mg)as an off-white solid. ¹H NMR (CD3OD) δ: 9.04-9.13 (m, 1H), 8.67 (s,1H), 8.17 (d, J=15.8 Hz, 1H), 8.00-8.13 (m, 2H), 7.66 (td, J=6.9, 1.4Hz, 1H), 7.42-7.58 (m, 4H), 7.21 (d, J=15.8 Hz, 1H); ES⁺ (M+H)⁺ 279.2

Compound Structure aldehyde diamine A1 

A2 

A3 

A4 

A5 

A6  (salt)

A7 

A8 

A9  (salt)

A10

A11

A12

Compound MS NMR A1  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 7.57 (d, J = 15.1 Hz,1H), 7.52-7.62 (m, 1H), 7.20 (dd, J = 8.0, 1.4 Hz, 1H), 6.99 260 (d, J =15.1 Hz, 1H), 7.04 (ddd, J = 8.0, 7.6, 1.4 Hz, 1H), 6.87 (dd, J = 8.0,1.4 Hz, 1H), 6.74 (td, J = 7.6, 1.4 Hz, 1H), 2.67-2.79 (m, 3H) A2  ES⁺(M + H)⁺ ¹H NMR (CD₃OD) δ: 7.88 (s, 1H), 7.77 (s, 1H), 7.54 (d, J = 15.7Hz, 1H), 7.17 (dd, J = 7.6, 1.4 Hz, 243 1H), 7.04 (td, J = 7.8, 1.4 Hz,1H), 6.87 (dd, J = 8.0, 1.5 Hz, 1H), 6.74 (td, J = 7.6, 1.4 Hz, 1H),6.57 (d, J = 15.7 Hz, 1H), 3.90 (s, 3H) A3  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD)δ: 7.50 (d, J = 15.7 Hz, 1H), 7.21 (dd, J = 7.7, 1.4 Hz, 1H), 7.05 (td,J = 8.1, 1.5 Hz, 260 1H), 6.98 (d, J = 15.7 Hz, 2H), 6.87 (dd, J = 8.0,1.4 Hz, 1H), 6.73 (td, J = 8.0, 1.4 Hz, 1H), 6.55 (s, 1H), 2.31 (s, 1H)A4  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.01 (s, 1H), 7.48 (d, J = 15.4 Hz,1H), 7.18 (dd, J = 7.7, 1.4 Hz, 1H), 7.04 (ddd, 244 J = 8.0, 7.3, 1.4Hz, 1H), 6.84 (d, J = 15.4 Hz, 1H), 6.86 (dd, J = 8.0, 1.4 Hz, 1H), 6.73(td, J = 7.6, 1.4 Hz, 1H), 2.49 (s, 3H) A5  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD)δ: 7.49 (d, J = 15.7 Hz, 1H), 7.21 (dd, J = 8.0, 1.5 Hz, 1H), 7.04 (ddd,J = 8.0, 7.7, 244 1.5 Hz, 1H), 6.98 (d, J = 15.7 Hz, 1H), 6.86 (dd, J =8.0, 1.5 Hz, 1H), 6.73 (td, J = 7.7, 1.4 Hz, 1H), 6.55 (s, 1H), 2.31 (s,3H) A6  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 9.09 (dt, J = 7.1, 0.8 Hz, 1H),8.67 (s, 1H), 8.17 (d, J = 15.7 Hz, 1H), 8.10 (ddd, (salt) 279 J = 9.1,6.9, 1.1 Hz, 1H), 8.03 (dt, J = 9.1, 1.2 Hz, 1H), 7.66 (td, J = 6.9, 1.4Hz, 1H), 7.43-7.60 (m, 4H), 7.21 (d, J = 15.7 Hz, 1H) A7  ES⁺ (M + H)⁺¹H NMR (CD₃OD) δ: 7.59 (d, J = 2.5 Hz, 1H), 7.57 (d, J = 15.8 Hz, 1H),7.19 (dd, J = 7.7, 1.4 Hz, 1H), 243 7.04 (td, J = 7.6, 1.4 Hz, 1H), 6.86(dd, J = 8.1, 1.2 Hz, 1H), 6.78 (d, J = 15.8 Hz, 1H), 6.74 (td, J = 7.7,1.4 Hz, 1H), 6.59 (d, J = 2.5 Hz, 1H), 3.90 (s, 3H) A8  ¹H NMR (CD₃OD)δ: 8.50 (d, J = 6.6 Hz, 1H), 7.73 (d, J = 15.9 Hz, 1H), 7.64 (d, J = 8.8Hz, 1H), 7.17- 7.29 (m, 2H), 7.06 (d, J = 15.7 Hz, 2H), 7.05 (ddd, J =8.0, 7.5, 1.5 Hz, 1H), 6.83-6.97 (m, 3H), 6.75 (td, J = 7.7, 1.4 Hz, 1H)A9  ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.82 (dt, J = 7.0, 1.1 Hz, 1H), 8.58(s, 1H), 8.06 (ddd, J = 9.1, 7.0, 1.1 Hz, 1H), (salt) 279 7.96 (dt, J =9.1, 0.8 Hz, 1H), 7.84 (d, J = 15.9 Hz, 1H), 7.45-7.57 (m, 5H), 7.22 (d,J = 15.9 Hz, 1H) A10 ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.11 (s, 1H), 7.78(d, J = 15.4 Hz, 1H), 7.70 (d, J = 1.4 Hz, 1H), 7.30 (d, J = 1.4 285 Hz,1H), 7.20 (dd, J = 7.8, 1.5 Hz, 1H), 7.04 (ddd, J = 8.2, 7.7, 1.4 Hz,1H), 6.87 (dd, J = 8.2, 1.4 Hz, 1H), 6.74 (ddd, J = 7.8, 7.7, 1.4 Hz,1H), 6.56 (d, J = 15.4 Hz, 1H) A11 ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.53(s, 1H), 8.03 (s, 1H), 7.78 (d, J = 8.5 Hz, 2H), 7.64 (d, J = 15.7 Hz,1H), 7.51 305 (t, J = 7.8 Hz, 2H), 7.35 (t, J = 7.7 Hz, 1H), 7.19 (d, J= 7.7 Hz, 1H), 7.04 (t, J = 7.6 Hz, 1H), 6.88 (d, J = 8.0 Hz, 1H), 6.69(d, J = 15.7 Hz, 1H), 6.74 (t, J = 7.7 Hz, 1H) A12 ES⁺ (M + H)⁺ ¹H NMR(CD₃OD) δ: 7.69 (s, 1H), 7.51 (d, J = 15.4 Hz, 1H), 7.37 (s, 1H), 7.19(dd, J = 7.8, 1.2 Hz, 243 1H), 7.03 (dt, J = 8.1, 1.4 Hz, 1H), 6.86 (dd,J = 8, 1.4 Hz, 1H), 6.74 (d, J = 15.4 Hz, 1H), 6.74 (dt, J = 8, 1.2 Hz,1H), 3.73 (s, 3H)Method B

Compounds described herein, where n=1, and R1, X, R2, R3, R4, R5, Ar/Hetare defined as defined anywhere herein, can be via preparation of theadvanced intermediate Ar/Het-CR4=CR5-CO—NH—C₆H₂R2R3(NH—P) where P is aprotecting group, as defined in, for example, Wuts P G M and Greene T W,2006, Greene's Protective Groups in Organic Synthesis, Fourth Edition,John Wiley & Sons, Inc., Hoboken, N.J., USA, and NH—P is ortho to theCO—NH group, i.e. in positions 1 and 2 of the aromatic ring.

Thus a Wittig or Horner-Wadsworth-Emmons carboxylic acid reagent,prepared by methods well known to those skilled in the art such as theArbuzov reaction, can be reacted with a suitably mono-protectedsubstituted or unsubstituted o-phenylenediamine. This compound is thenreacted with a monocyclic or bicyclic heterocyclic aldehyde or ketone toform the corresponding γ-substituted acrylamide. This advancedintermediate can be derivatized to generate compounds of the inventionby reaction with different R1-X-containing reagents using couplingtechniques well known to those skilled in the art such as, but notlimited to, Suzuki coupling, Heck coupling, alkylation, acylation. Thesame intermediate can also be simply deprotected to form the compoundwhere R1 is H and X is a single bond.

Example 2: Advanced intermediate (E)-tert-butyl(2-(3-(1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

tert-butyl (2-(2-(diethoxyphosphoryl)acetamido)phenyl)carbamate

DIPEA (5.16 g, 6.90 mL, 40 mmol) and tert-butyl 2-aminophenylcarbamate(2.08 g, 10 mmol) were added to a solution of2-(diethoxyphosphoryl)acetic acid (2.15 g, 11 mmol) in DCM (120 mL).After the mixture was stirred for ten minutes, HATU (4.56 g, 12 mmol)was added to the reaction and stirring was prolonged for 6 h at roomtemperature under a nitrogen atmosphere. After completion of thereaction as indicated by HPLC, the reaction mixture was washed withsaturated NaHCO₃ and brine. It was dried over Na₂SO₄ and filtered. Thefiltrate was evaporated in vacuo to get the crude product, which wastriturated with 30% v/v hexanes in EtOAc for 30 min. The solid wasfiltered, washed with 30% hexanes in EtOAc and dried to get 2.92 g oftert-butyl (2-(2-(diethoxyphosphoryl)acetamido)phenyl)carbamate as anoff-white solid in 76% yield.

¹HNMR (300 MHz, CD₃OD): δ 7.64 (d, 1H, J=8.4 Hz), 7.37 (dd, 1H, J=1.8Hz, 8.1 Hz), 7.07-7.24 (m, 2H), 4.20 (m, 4H), 3.15 (d, 2H, J=21.9 Hz),1.51 (s, 9H), 1.35 (t, 6H, J=6.9 Hz), MS: ES⁺ (M+Na)⁺: 410

(E)-tert-butyl (2-(3-(1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

A 60% suspension of NaH in paraffin oil (192 mg, 5 mmol) was addedportionwise to a solution of tert-butyl(2-(2-(diethoxyphosphoryl)acetamido)phenyl)carbamate (1.93 g, 5 mmol) inanhydrous THF (25 mL) at 0° C. The reaction mixture was stirred for 30min before being warmed up to room temperature.1H-pyrazole-4-carbaldehyde (400 mg, 4.16 mmol) dissolved in anhydrousTHF (5 mL) was then added and the reaction mixture was stirred for 72 hunder a nitrogen atmosphere. After completion of the reaction asindicated by HPLC, the mixture was diluted with EtOAc (80 mL) andquenched with a saturated NH₄Cl solution (10 mL). The organic layer wasseparated and washed with water (40 mL) and brine (20 mL). It was driedover anhydrous Na₂SO₄ and the solid was filtered. The filtrate wasevaporated under vacuum. The isolated crude was purified by silica gelcolumn chromatography using a gradient of 0-100% EtOAc in hexanes toprovide 986 mg of (E)-tert-butyl(2-(3-(1H-pyrazol-4-yl)acrylamido)phenyl)carbamate as a white solid.¹HNMR (300 MHz, CD₃OD): δ 7.93 (broad s, 2H), 7.64 (d, 1H, J=15.6 Hz),7.56 (d, 1H, J=7.2 Hz), 7.45 d, 1H, J=7.8 Hz), 7.11-7.24 (m, 2H), 6.59(d, 1H, J=15.6 Hz), 1.50 (s, 9H), MS: ES⁺ (M+Na)⁺: 351

Example 3: Hydrochloride salt of(E)-N-(2-aminophenyl)-3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamideB5

(E)-tert-butyl(2-(3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

Cesium carbonate (98 mg, 0.30 mmol) was added to a solution of(E)-tert-butyl (2-(3-(1H-pyrazol-4-yl)acrylamido)phenyl)carbamate (100mg, 0.30 mmol) in anhydrous DMF (4 mL). A solution of1-(2-bromoethoxy)-3-chloro-5-fluorobenzene (76 mg, 0.30 mmol) in DMF (1mL) was then added and the reaction mixture was stirred overnight atroom temperature under a nitrogen atmosphere. It was diluted with EtOAc(30 mL) and washed with water (2×40 mL) and brine (10 mL). The organiclayer was dried over anhydrous Na₂SO₄ and filtered. The evaporated crudewas purified by silica gel column chromatography using a gradient of0-100% of EtOAc in hexanes to provide 144 mg of (E)-tert-butyl(2-(3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamateas a white solid. MS: ES⁺ (M+Na)⁺: 523

(E)-N-(2-aminophenyl)-3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamide

A 4 M solution of HCl in dioxane (2 mL) was added to a solution of(E)-tert-butyl(2-(3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate(118 mg, 0.23 mmol) in dioxane (3 mL) and the mixture was stirred for 6h at room temperature under a nitrogen atmosphere. The reaction mixturewas then diluted with EtOAc (15 mL). The salt was filtered, washed withEtOAc and dried overnight to give 99 mg of the hydrochloric acid salt of(E)-N-(2-aminophenyl)-3-(1-(2-(3-chloro-5-fluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamideas an off-white solid. MS: ES⁺ (M+Na)⁺: 423

Example 4: hydrochloride salt of(E)-N-(2-aminophenyl)-3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamideB3 (E)-tert-butyl (2-(3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

As described for the synthesis of B5 above, cesium carbonate (64 mg,0.27 mmol) followed by a solution of1-(2-bromoethoxy)-3,5-difluorobenzene (76 mg, 0.30 mmol) in DMF (1 mL)were added to a solution of (E)-tert-butyl(2-(3-(1H-pyrazol-4-yl)acrylamido)phenyl)carbamate (90 mg, 0.27 mmol) inanhydrous DMF (4 mL). The reaction mixture was stirred overnight at roomtemperature under a nitrogen atmosphere. It was then diluted with 30 mLEtOAc and washed with water (2×40 mL) and brine (10 mL). The organiclayer was dried over anhydrous Na₂SO₄ and filtered. The concentratedfiltrate was purified by silica gel column chromatography using agradient of 0-100% of EtOAc in hexanes to provide, after evaporationunder reduced pressure of pooled fractions, 123 mg of (E)-tert-butyl(2-(3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamateas a white solid. MS: ES⁺ (M+Na)⁺: 507

(E)-N-(2-aminophenyl)-3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamide

A solution of (E)-tert-butyl(2-(3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate(113 mg, 0.23 mmol) in dioxane (3 mL) was mixed with a 4 M solution ofHCl in dioxane (2 mL). The mixture was stirred for 6 h at roomtemperature under a nitrogen atmosphere. The reaction mixture was thendiluted with ethylaceate (15 mL). The salt was filtered, washed withEtOAc and dried overnight to 92 mg of the hydrochloric acid salt of(E)-N-(2-aminophenyl)-3-(1-(2-(3,5-difluorophenoxy)ethyl)-1H-pyrazol-4-yl)acrylamideas an off-white solid. MS: ¹H NMR (CD₃OD) δ: 8.07 (s, 1H), 7.86 (s, 1H),7.70 (d, J=15.4 Hz, 1H), 7.28-7.54 (m, 4H), 6.62 (d, J=15.7 Hz, 1H),6.45-6.57 (m, 3H), 4.55 (t, J=5.2 Hz, 2H), 4.37 (t, J=5.2 Hz, 2H) ES⁺(M+Na)⁺: 407

TABLE Method B Compound Structure R1—X-coupling reagent B1 (salt)

B2 (salt)

B3 (salt)

B4 (salt)

B5 (salt)

B6

Compound MS NMR B1 ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.13 (s, 1H), 7.91 (s,1H), 7.72 (d, J = 15.7 Hz, 1H), 7.30-7.62 (m, 4H), 6.65 (d, (salt) 283 J= 15.7 Hz, 1H), 4.05 (d, J = 7.1 Hz, 2H), 1.17-1.46 (m, 1H), 0.56-0.82(m, 2H), 0.36-0.49 (m, 2H) B2 ES⁺ (M + H)⁺ ¹H NMR (CD₃OD) δ: 8.08 (s,1H), 7.90 (s, 1H), 7.73 (d, J = 15.7 Hz, 1H), 7.34-7.58 (m, 6H), 7.05(t, (salt) 363 J = 9.1 Hz, 2H), 6.63 (d, J = 15.7 Hz, 1H), 6.63 (dd, J =15.7, 0.8 Hz, 1H), 6.38 (dt, J = 15.7, 6.3 Hz, 1H), 4.95 (dd, J = 6.3,0.8 Hz, 2H) B3 ES⁺ (M + Na)⁺: ¹H NMR (CD₃OD) δ: 8.07 (s, 1H), 7.86 (s,1H), 7.70 (d, J = 15.4 Hz, 1H), 7.28-7.54 (m, 4H), 6.62 (d, (salt) 407 J= 15.7 Hz, 1H), 6.45-6.57 (m, 3H), 4.55 (t, J = 5.2 Hz, 2H), 4.37 (t, J= 5.2 Hz, 2H) B4 ES⁺ (M + Na)⁺: ¹H NMR (CD₃OD) δ: 8.09 (s, 1H), 7.87 (s,1H), 7.72 (d, J = 15.7 Hz, 1H), 7.57 (d, J = 8.8 Hz, 2H), (salt) 4297.40-7.54 (m, 3H), 7.37 (dd, J = 8.0, 1.5 Hz, 1H), 7.06 (d, J = 8.8 Hz,2H), 6.61 (d, J = 15.7 Hz, 1H), 4.59 (t, J = 5.2 Hz, 2H), 4.45 (t, J =5.2 Hz, 2H) B5 ES⁺ (M + Na)⁺: ¹H NMR (CD₃OD) δ: 8.07 (s, 1H), 7.87 (s,1H), 7.71 (d, J = 15.7 Hz, 1H), 7.32-7.57 (m, 4H), 6.77 (dt, (salt) 423J = 8.2, 2.2 Hz, 1H), 6.78 (d, J = 2.2 Hz, 1H), 6.61 (d, J = 15.9 Hz,1H), 6.66 (dt, J = 10.7, 2.2 Hz, 1H), 4.55 (t, J = 5.2 Hz, 2H), 4.38 (t,J = 5.2 Hz, 2H) B6 ES⁺ (M + Na)⁺: ¹H NMR (CD₃OD) δ: 8.00 (s, 1H), 7.82(s, 1H), 7.55 (d, J = 15.7 Hz, 1H), 7.17 (dd, J = 8.0, 1.4 Hz, 367 1H),6.92-7.07 (m, 3H), 6.82-6.92 (m, 3H), 6.73 (td, J = 7.6, 1.4 Hz, 1H),6.58 (d, J = 15.7 Hz, 1H), 4.51 (t, J = 5.2 Hz, 1H), 4.31 (t, J = 5.2Hz, 1H)Method C

Compounds described herein, where n=1 and R2, R3, R4, R5 are defined asanywhere herein, where Ar/Het is a mono or bicyclic heterocycle with afree amino group, and R6 stands for R1-X, can be prepared using a HomerWadsworth Emmons approach where the corresponding heterocyclic aldehydeor ketone, such as, but not limited to, 1H-pyrazole-3-carbaldehyde,1H-pyrazole-4-carbaldehyde, 1-(1H-pyrazol-4-yl)ethanone,1H-imidazole-4-carbaldehyde, is reacted with a dialkoxyphosphono aceticacid ester to give the corresponding 7-(N-alkylheterocycle)acrylateester. The ester can be hydrolyzed and the acid reacted with a protectedor unprotected substituted or unsubstituted o-phenylenediamine to givecompounds of the invention after deprotection if required using methodswell known to those skilled in the art and which are described forexample in P. G. M. Wuts and T. W. Greene, 2006, Greene's ProtectiveGroups in Organic Synthesis, Fourth Edition, John Wiley & Sons, Inc.,Hoboken, N.J., USA.

Example 5:(E)-N-(2-amino-5-fluorophenyl)-3-(1-methyl-1H-pyrazol-4-yl)acrylamide C2

(E)-methyl 3-(1-methyl-1H-pyrazol-4-yl)acrylate

Cs₂CO₃ (1.304 g, 4 mmol) was added to a solution of1H-pyrazole-4-carbaldehyde (0.192 g, 2 mmol) in dioxane (8 mL) at roomtemperature. Trimethylphosphonoacetate (0.364 g, 0.40 mmol) was added tothis suspension, followed by DMSO (2 mL). The reaction mixture washeated to 100° C. overnight. It was then diluted with EtOAc (40 mL), andwashed with water (40 mL) and brine (20 mL). The organic layer wasconcentrated under vacuum. The crude was purified by silica gel columnchromatography using a 0-100% gradient of EtOAc in hexanes to provide(E)-methyl 3-(1-methyl-1H-pyrazol-4-yl)acrylate (0.278 g). ES⁺ (M+H)⁺167

(E)-3-(1-methyl-1H-pyrazol-4-yl)acrylic acid

(E)-methyl 3-(1-methyl-1H-pyrazol-4-yl)acrylate (0.24 g, 1.45 mmol) wasdissolved in MeOH (10 mL). A 1M solution of KOH (5.8 mL) was added andthe mixture was heated at 70° C. overnight. The reaction mixture wasthen evaporated under reduced pressure and water (10 mL) was added tothe residue. This solution was carefully acidified to pH 4 with a 3Maqueous solution of HCl. The carboxylic acid precipitated and wasextracted with ethyl acetate. The EtOAc layer was washed with water(2×10 mL) and brine (1×15 mL). It was dried over sodium sulfate,filtered and evaporated under vacuum to give(E)-3-(1-methyl-1H-pyrazol-4-yl)acrylic acid as a white solid (160 mg).ES⁺ (M+H)⁺ 153

(E)-tert-butyl(5-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

DIPEA (0.16 g, 1.20 mmol), 4-fluoro-tert-butyl-2-aminophenylcarbamate(0.14 g, 0.64 mmol) and HATU (0.20 g, 0.52 mmol) were added to asolution of (E)-3-(1-methyl-1H-pyrazol-4-yl)acrylic acid (0.061 g, 0.401mmol) in DCM (10 mL). The reaction mixture was stirred overnight at roomtemperature under nitrogen. After completion of the reaction asindicated by HPLC, the organic solution was washed with saturated NaHCO₃then brine. It was dried over Na₂SO₄ and the solvent was evaporated.Crude (E)-tert-butyl(5-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate waspurified by column chromatography using a 20-80% gradient of EtOAc inhexanes to give the title compound (0.15 g) as an off-white solid. ES⁺(M+H)⁺ 361.

(E)-N-(2-amino-4-fluorophenyl)-3-(1-methyl-M-pyrazol-4-yl)acrylamide

(E)-tert-butyl(5-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate(0.15 g, 0.42 mmol) was dissolved in dioxane (4 mL). A 4M solution ofHCl in dioxane (4 mL) was added and the mixture was stirred at roomtemperature for 3 h. Salt precipitation was observed. The reactionmixture was then diluted with diethyl ether (20 mL) and the crudehydrochloride salt was filtered. It was stirred with saturated sodiumbicarbonate (excess) and filtered. The precipitate was washed with waterand vacuum dried.(E)-N-(2-amino-4-fluorophenyl)-3-(1-methyl-1H-pyrazol-4-yl)acrylamide(73 mg) was obtained as an off-white solid. ¹H NMR (CD₃OD) δ: 7.88 (s,1H), 7.77 (s, 1H), 7.53 (d, J=15.7 Hz, 1H), 7.12 (dd, J=8.5, 5.9 Hz,1H), 6.54 (d, J=15.9 Hz, 1H), 6.55 (dd, J=10.5, 3.0 Hz, 1H), 6.39 (td,J=8.5, 2.7 Hz, 1H), 3.90 (s, 4H); ES⁺ (M+H)⁺ 261.

Example 6:(E)-N-(2-amino-4-fluorophenyl)-3-(1-methyl-1H-pyrazol-4-yl)acrylamide C3(E)-tert-butyl(4-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate

The protocol described above for the synthesis of (E)-tert-butyl(4-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido)phenyl)carbamate wasused substituting 4-fluoro-tert-butyl-2-aminophenylcarbamate (0.14 g,0.64 mmol) for the 5-fluoro analog. Thus starting from(E)-3-(1-methyl-1H-pyrazol-4-yl)acrylic acid (0.061 g, 0.401 mmol) inDCM (10 mL), 0.10 g of pure (E)-tert-butyl(4-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido) phenyl)carbamatewere obtained as an off-white solid after silica gel chromatography. ES⁺(M+H)⁺ 361.

(E)-N-(2-amino-5-fluorophenyl)-3-(1-methyl-1H-pyrazol-4-yl)acrylamide

Protecting group removal was effected by addition of a 4M solution ofHCl in dioxane (2.5 mL) to a solution of (E)-tert-butyl(4-fluoro-2-(3-(1-methyl-1H-pyrazol-4-yl)acrylamido) phenyl)carbamate(0.10 g, 0.28 mmol) in dioxane (2.5 mL). The mixture was stirred at roomtemperature for 3 h. The reaction mixture was diluted with diethyl ether(20 mL) and the hydrochloride salt of(E)-N-(2-amino-5-fluorophenyl)-3-(1-methyl-1H-pyrazol-4-yl)acrylamideprecipitated was filtered. It was suspended in a saturated sodiumbicarbonate solution and the mixture was stirred. The solid was filteredand washed with water then dried under vacuum to give the pure product(58 mg) as an off-white solid. ES⁺ (M+H)⁺ 261.

TABLE method 3 Com- pound Structure R—(RO)₂P(O)CH₂CO₂R diamine MS NMR C1

CH₃—CH₂—

ES⁺ (M + H)⁺ 257 ¹H NMR (CD₃OD) δ: 7.94 (s, 1H), 7.79 (s, 1H), 7.55 (d,J = 15.7 Hz, 1H), 7.17 (dd, J = 8.0, 1.1 Hz, 1H), 7.04 (td, J = 7.7, 1.4Hz, 1H), 6.87 (dd, J = 8.0, 1.4 Hz, 1H), 6.74 (td, J = 7.7, 1.4 Hz, 1H),6.57 (d, J = 15.7 Hz, 1H), 4.20 (q, J = 7.4 Hz, 2H), 1.47 (t, J = 7.4Hz, 3H) C2

CH₃—

ES⁺ (M + H)⁺ 261 ¹H NMR (CD₃OD) δ: 7.88 (s, 1H), 7.77 (s, 1H), 7.53 (d,J = 15.7 Hz, 1H), 7.12 (dd, J = 8.5, 5.9 Hz, 1H), 6.54 (d, J = 15.7 Hz,1H), 6.55 (dd, J = 10.5, 3.0 Hz, 1H), 6.39 (td, J = 8.5, 2.7 Hz, 1H),3.90 (s, 3H) C3

CH₃—

ES⁺ (M + H)⁺ 261 ¹H NMR (CD₃OD) δ: 7.89 (s, 1H), 7.77 (s, 1H), 7.56 (d,J = 15.7 Hz, 1H), 7.13 (dd, J = 9.9, 2.7 Hz, 1H), 6.78 (td, J = 8.5, 2.7Hz, 1H), 6.84 (dd, J = 8.8, 5.8 Hz, 1H), 6.56 (d, J = 15.7 Hz, 1H), 3.90(s, 3H)Method D

Compounds described herein, where n=1, and R1, X, R2, R3, R4, R5, andAr/Het are defined as defined anywhere herein, can be prepared byreaction of a mono or bicyclic heterocycle aldehyde or ketone, which canbe prepared by methods well known to those skilled in the art anddetailed in, for example, Joule J A and Mills K, Heterocyclic Chemistry,Fifth Edition, John Wiley & Sons, Inc., Hoboken, N.J., USA, with adialkoxyphosphoryl acetic acid ester or a trialkyl, or triphenylphosphoranylidene acetic acid ester to give the correspondingγ-(heterocycle)acrylate ester Ar/Het-CR4=CR5-COOR7. The R1-X— moiety canthen be added to this intermediate by synthetic methods well known tothose skilled in the art, including but not limited to Heck coupling,Suzuki reaction, alkylation, acylation. Alternatively the R1-X—substituent can be coupled to the aldehyde or ketone prior to the Wittigor Horner-Wadsworth-Emmons reaction to give the same intermediate ester.The ester can then be hydrolyzed and the acid reacted with a protectedor unprotected substituted or unsubstituted o-phenylenediamine to givecompounds of the invention after deprotection if required using methodswell known to those skilled in the art and which are described forexample in P. G. M. Wuts and T. W. Greene, 2006, Greene's ProtectiveGroups in Organic Synthesis, Fourth Edition, John Wiley & Sons, Inc.,Hoboken, N.J., USA.

Example 7:(E)-N-(2-aminophenyl)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylamideD3

Or alternatively

(E)-ethyl 3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylate

Cesium carbonate (0.490 g, 1.5 mmol) and 1-(2-bromoethoxy)benzene (0.261g, 1.30 mmol) were added to a solution of (E)-ethyl3-(1H-pyrazol-4-yl)acrylate (0.167 g, 1 mmol) in ACN (8 mL) at roomtemperature. The suspension was stirred overnight at 80° C. The reactionmixture was then cooled down to room temperature and the precipitatedsolids were filtered off. The filtrate was concentrated and purified bysilica gel column chromatography using a gradient of 0-60% of EtOAc inhexanes to provide the title compound (0.203 g, 71%) as a colorless oil.ES⁺ (M+H)⁺ 287

(E)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylic acid

To a solution of (E)-ethyl3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylate (0.143 g, 0.5 mmol) inEtOH (6 mL) was added KOH (0.168 g, 3 mmol) in water (2 mL) and thesolution was heated at 60° C. for 6 h. The reaction mixture was thenevaporated under vacuum and water (10 mL) was added to the residue. Thissolution was acidified to pH 4 with aqueous 3N HCl and extracted withEtOAc. The organic extracts were washed with water and brine, dried overNa₂SO₄ and evaporated in vacuo to get the acid (0.117 g, 91%) as a whitesolid. ES⁺ (M+H)⁺ 259

Alternate synthesis: 1-(2-phenoxyethyl)-1H-pyrazole-4-carbaldehyde

Sodium hydride (60%, 6.3 g, 1.0 eq) was added to a solution of1H-pyrazole-4-carbaldehyde (15 g, 156 mmol) in DMF (150 ml) at 0° C. Themixture was allowed to warm and was stirred at room temperature.(2-Bromoethoxy)benzene (30.2 g, 1 eq) was then added and the resultingmixture was stirred overnight at room temperature. It was quenched byaddition of aqueous ammonium chloride, diluted with water and extractedwith EtOAc. The combined organic layers were dried over Na₂SO₄,filtered, and concentrated. The residue was purified by columnchromatography using a hexane/EtOAc gradient (10:1 to 0:100). Purefractions were combined and evaporated under reduced pressure to yield1-(2-phenoxyethyl)-1H-pyrazole-4-carbaldehyde (24 g, 71%).

Alternate Synthesis: (E)-methyl3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylate

Trimethyl phosphonoacetate (20.6 g, 112 mmol) was dissolved in 350 mLTHF. A 25% w/w NaOMe solution (25 mL) was then added at room temperatureand the resulting mixture was stirred for 30 min.1-(2-Phenoxyethyl)-1H-pyrazole-4-carbaldehyde (24 g, 111 mmol) dissolvedin 150 mL THF was added and the reaction mixture was stirred for 5 hbefore being quenched with aqueous ammonium chloride and extracted withEtOAc. The combined organic layers were dried over Na₂SO₄, filtered, andconcentrated under vacuum. The residue was purified by columnchromatography using a gradient of hexane/EtOAc (30:1 to 1:2) to yield(E)-methyl 3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylate (22 g, 72.7%).

Alternate synthesis: (E)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylicacid

A 3M aqueous solution of NaOH (80 mL) was added to a solution of(E)-methyl 3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylate (22 g, 81mmol) in MeOH (150 mL) at room temperature and the mixture was stirredovernight. The solvent was evaporated under reduced pressure. Theconcentrated solution was washed with diethylether, acidified to pH=2with dilute HCl, and extracted with dichloromethane. The combinedorganic extracts were washed with water and brine, before being driedover Na₂SO₄. Salts were filtered and washed and the filtrate wasevaporated under reduced pressure. The product precipitated from theconcentrated solution upon standing. It was filtered and dried undervacuum to give the corresponding(E)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylic acid (18 g, 86%).

(E)-N-(2-aminophenyl)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylamide,D3

HATU (0.228 g, 0.60 mmol), DIPEA (0.258 g, 2.00 mmol) ando-phenylenediamine (0.129 g, 1.20 mmol) were added to a solution of((E)-3-(1-(2-phenoxyethyl)-1H-pyrazol-4-yl)acrylic acid (0.103 g, 0.40mmol) in DCM (25 mL). The solution was stirred overnight at roomtemperature. Solvents were evaporated in vacuo and the residue was takenup in EtOAc (40 mL). This solution was washed with saturated NaHCO₃ andbrine, dried (Na₂SO₄) and evaporated. The crude product was purified bysilica gel column chromatography (gradient of 0-80% EtOAc in hexanes) toget D3 as an off-white solid (0.094 g, 68%). ¹H NMR (CD₃OD) δ: 8.01 (s,1H), 7.82 (s, 1H), 7.55 (d, J=15.8 Hz, 1H), 7.21-7.31 (m, 2H), 7.17 (dd,J=8.0, 1.1 Hz, 1H), 7.03 (td, J=7.8, 1.2 Hz, 1H), 6.81-6.97 (m, 4H),6.73 (td, J=7.6, 1.4 Hz, 1H), 6.58 (d, J=15.7 Hz, 1H), 4.53 (t, J=5.1Hz, 2H), 4.34 (t, J=5.0 Hz, 2H); ES⁺ (M+H)⁺ 349.

Example 8: hydrochloride salt of(E)-N-(2-amino-4-fluorophenyl)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamideD2

(E)-ethyl 3-(1H-pyrazol-4-yl)acrylate

[(Ethoxycarbonyl)methylene]triphenylphosphorane (0.836 g, 2.4 mmol) wasadded to a solution of 1H-pyrazole-4-carbaldehyde (0.192 g, 2 mmol) inTHF (6 mL) at room temperature. This solution was heated at 70° C. underanitrogen atmosphere for 8 h. HPLC/MS analysis indicated completion ofthe reaction and both E and Z isomers of product were observed. Thereaction mixture was cooled down to room temperature and evaporated invacuo to get the crude product. This crude was purified by silica gelcolumn chromatography using 0-80% EtOAc in hexanes as eluent to provide,after evaporation of pooled fractions, pure (E)-ethyl3-(1H-pyrazol-4-yl)acrylate (0.198 g, 60%) as a white solid. ES⁺ (M+H)⁺167

(E)-ethyl 3-(1-cinnamyl-1H-pyrazol-4-yl)acrylate

Cesium carbonate (0.490 g, 1.5 mmol) was added to a solution of(E)-ethyl 3-(1H-pyrazol-4-yl)acrylate (0.167 g, 1 mmol) in ACN (8 mL) atroom temperature. The suspension was stirred and1-((E)-3-bromoprop-1-enyl)benzene (0.256 g, 1.30 mmol) was added. Themixture was heated at 40° C. overnight. After cooling down to roomtemperature, the precipitated solids were filtered off. The filtrate wasconcentrated and purified by silica gel column chromatography using a0-60% gradient of EtOAc in hexanes to provide the title compound as acolorless oil (0.214 g, 76%). ES⁺ (M+H)⁺ 283

(E)-3-(1-cinnamyl-1H-pyrazol-4-yltacrylic acid

The ethyl ester of (E)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylic acid (0.141g, 0.5 mmol) dissolved in ethanol (EtOH, 6 mL) was hydrolyzed byaddition of a solution of KOH (0.168 g, 3 mmol) in water (2 mL). Themixture was heated to 60° C. and the temperature was maintained for 6 h.Solvents were then evaporated under vacuum and water (10 mL) was addedto the residue. This solution was carefully acidified to pH 4 with a 3Msolution of HCl in water and extracted with EtOAc. The organic layer waswashed with water and brine. It was dried (Na₂SO₄), filtered andevaporated to give the acid as a white solid (0.118 g, 93%). ES⁺ (M+H)⁺255

tert-Butyl(24(E)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamido)-5-fluorophenyl)carbamate

(E)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylic acid (0.110 g, 0.43 mmol) wasdissolved in DCM (25 mL). HATU (0.246 g, 0.65 mmol), DIPEA (0.278 g,2.15 mmol) and tert-butyl 2-amino-5-fluorophenylcarbamate (0.147 g, 0.65mmol) were added and the mixture was stirred overnight at roomtemperature under nitrogen. Solvents were evaporated and the residue wastaken up in EtOAc (40 mL). It was then washed with saturated NaHCO₃ andbrine, dried over Na₂SO₄, filtered and evaporated in vacuo to get thecrude. The product was purified by silica gel column chromatographyusing a gradient of 0-70% EtOAc in hexanes to get tert-butyl(24(E)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamido)-5-fluorophenyl)carbamate5(0.138 g, 76%) as an off-white solid. ES⁺ (M+Na)⁺ 485.

Hydrochloride salt of(E)-N-(2-amino-4-fluorophenyl)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamide

A 4M solution of HCl in dioxane (4 mL) was mixed under nitrogen with asolution of tert-butyl(2-((E)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamido)-5-fluorophenyl)carbamate(0.138 g, 0.30 mmol) in dioxane (12 mL). The mixture was stirred for 4 hat room temperature under nitrogen. Salt precipitation was observed. Theheterogeneous mixture was diluted with EtOAc (12 mL) and the precipitatewas filtered, washed with solvent and dried overnight under vacuum toget the pure hydrochloride salt of(E)-N-(2-amino-4-fluorophenyl)-3-(1-cinnamyl-1H-pyrazol-4-yl)acrylamide(0.110 g, 92%) as an off-white solid. ¹H NMR (CD₃OD) δ: 8.08 (s, 1H),7.90 (s, 1H), 7.71 (d, J=15.5 Hz, 1H), 7.37-7.46 (m, 2H), 7.21-7.37 (m,4H), 6.63 (d, J=15.7 Hz, 1H), 6.56-6.71 (m, 1H), 6.43 (dt, J=15.8, 6.2Hz, 1H), 4.96 (dd, J=6.3, 1.1 Hz, 2H); ES⁺ (M+H)⁺ 363

Com- pound Structure R1—X-coupling reagent D1 

D2 

D3 

D4 

D5 

D6 

D7 

D8 

D9 

D10

D11

D12

D13

D14

D15

D16

Com- pound diamine MS NMR D1 

ES⁺ (M + H)⁺ 345 ¹H NMR (CD₃OD) δ: 7.98 (s, 1H), 7.83 (s, 1H), 7.56 (d,J = 15.8 Hz, 1H), 7.36-7.46 (m, 2H), 7.20-7.36 (m, 3H), 7.17 (dd, J =8.1, 1.1 Hz, 1H), 7.03 (td, J = 7.7, 1.2 Hz, 1H), 6.86 (dd, J = 8.4, 1.2Hz, 1H), 6.73 (td, J = 7.7, 1.4 Hz, 1H), 6.62 (d, J = 15.8 Hz, 1H), 6.59(d, J = 15.7 Hz, 1H), 6.42 (dt, J = 15.8, 6.2 Hz, 1H), 4.93 (d, J = 6.2Hz, 2H) D2 

ES⁺ (M + H)⁺ 363 ¹H NMR (CD₃OD) - HCl salt - δ: 8.08 (s, 1H), 7.90 (s,1H), 7.71 (d, J = 15.5 Hz, 1H), 7.37-7.46 (m, 2H), 7.21-7.37 (m, 4H),6.63 (d, J = 15.7 Hz, 1H), 6.56-6.71 (m, 1H), 6.43 (dt, J = 15.8, 6.2Hz, 1H), 4.96 (dd, J = 6.3, 1.1 Hz, 2H) D3 

ES⁺ (M + H)⁺ 349 ¹H NMR (CD₃OD) δ: 8.01 (s, 1H), 7.82 (s, 1H), 7.55 (d,J = 15.8 Hz, 1H), 7.21-7.31 (m, 2H), 7.17 (dd, J = 8.0, 1.1 Hz, 1H),7.03 (td, J = 7.8, 1.2 Hz, 1H), 6.81-6.97 (m, 4H), 6.73 (td, J = 7.6,1.4 Hz, 1H), 6.58 (d, J = 15.7 Hz, 1H), 4.53 (t, J = 5.1 Hz, 2H), 4.34(t, J = 5.0 Hz, 2H) D4 

ES⁺ (M + H)⁺ 319 ¹H NMR (CD₃OD) δ: 7.98 (s, 1H), 7.82 (s, 1H), 7.55 (d,J = 15.7 Hz, 1H), 7.21-7.41 (m, 5H), 7.17 (dd, J = 7.8, 1.2 Hz, 1H),7.03 (ddd, J = 8.0, 7.8, 1.1 Hz, 1H), 6.86 (dd, J = 8.0, 1.4 Hz, 1H),6.73 (td, J = 7.7, 1.1 Hz, 1H), 6.58 (d, J = 15.7 Hz, 1H), 5.35 (s, 2H)D5 

ES⁺ (M + H)⁺ 337 ¹H NMR (CD₃OD) δ: 7.99 (s, 1H), 7.82 (s, 1H), 7.54 (d,J = 15.7 Hz, 1H), 7.24-7.38 (m, 2H), 7.17 (dd, J = 8.0, 1.4 Hz, 1H),6.99-7.13 (m, 2H), 7.03 (td, J = 7.6, 1.6 Hz, 1H), 6.86 (dd, J = 8.0,1.4 Hz, 1H), 6.73 (td, J = 7.6, 1.4 Hz, 1H), 6.58 (d, J = 15.7 Hz, 1H),5.33 (s, 2H) D6 

ES⁺ (M + H)⁺ 333 ¹H NMR (CD₃OD) δ: 8.07 (s, 1H), 7.85 (s, 1H), 7.68 (t,J = 7.7 Hz, 1H), 7.57 (d, J = 15.8 Hz, 1H), 7.22 (d, J = 7.7 Hz, 2H),7.18 (dd, J = 7.7, 1.2 Hz, 1H), 7.04 (td, J = 7.7, 1.8 Hz, 1H), 6.87(dd, J = 8.1, 1.4 Hz, 2H), 6.91 (d, J = 7.7 Hz, 1H), 6.74 (td, J = 7.6,1.5 Hz, 1H), 6.60 (d, J = 15.7 Hz, 1H), 5.42 (s, 2H), 2.53 (s, 3H) D7 

ES⁺ (M + H)⁺ 333 ¹H NMR (CD₃OD) δ: 7.80 (s, 1H), 7.62-7.71 (m, 1H), 7.47(d, J = 15.7 Hz, 1H), 7.13-7.26 (m, 4H), 7.07-7.13 (m, 2H), 7.03 (td, J= 7.7, 1.5 Hz, 1H), 6.86 (dd, J = 8.1, 1.5 Hz, 1H), 6.73 (td, J = 7.6,1.5 Hz, 1H), 6.51 (d, J = 15.7 Hz, 1H), 4.38 (t, J = 7.0 Hz, 2H), 3.14(t, J = 7.0 Hz, 2H) D8 

ES⁺ (M + H)⁺ 347 ¹H NMR (CD₃OD) δ: 7.92 (s, 1H), 7.81 (s, 1H), 7.55 (d,J = 15.7 Hz, 1H), 7.23-7.35 (m, 2H), 7.12-7.22 (m, 4H), 7.04 (td, J =7.8, 1.5 Hz, 1H), 6.87 (dd, J = 8.0, 1.4 Hz, 1H), 6.74 (td, J = 7.6, 1.4Hz, 1H), 6.57 (d, J = 15.7 Hz, 1H), 4.16 (t, J = 7.0 Hz, 3H), 2.60 (t, J= 7.7 Hz, 3H), 2.18 (tt, J = 7.7, 7.0 Hz, 3H) D9 

ES⁺ (M + H)⁺ 361 ¹H NMR (CD₃OD) δ: 7.90 (s, 1H), 7.79 (s, 1H), 7.54 (d,J = 15.7 Hz, 1H), 7.20-7.31 (m, 2H), 7.09-7.20 (m, 4H), 7.03 (td, J =7.5, 1.4 Hz, 1H), 6.87 (dd, J = 8.1, 1.2 Hz, 1H), 6.74 (td, J = 7.5, 1.5Hz, 1H), 6.56 (d, J = 15.7 Hz, 1H), 4.17 (t, J = 7.0 Hz, 2H), 2.63 (t, J= 7.6 Hz, 2H), 1.88 (quin, J = 7.0 Hz, 2H), 1.59 (tt, J = 7.6, 7.0 Hz,2H) D10

ES⁺ (M + H)⁺ 369 ¹H NMR (CD₃OD) δ: 7.85 (s, 1H), 7.78 (s, 1H), 7.5 (d, J= 15.6 Hz, 1H), 7.46-7.40 (m, 5H), 7.17 (dd, J = 8.1, 1.5 Hz, 1H), 7.04(td, J = 7.2, 1.5 Hz, 1H), 6.86 (dd, J = 8.1, 1.2 Hz, 1H), 6.73 (td, J =8.1, 1.2 Hz, 1H), 6.57 (d, J = 15.6 Hz, 1H), 4.84 (t, J = 13.5 Hz, 2H)D11

ES⁺ (M + H)⁺ 359 ¹H NMR (CD₃OD) δ: 7.94 (s, 1H), 7.81 (s, 1H), 7.53 (d,J = 15.7 Hz, 1H), 7.21-7.39 (m, 4H), 7.11-7.21 (m, 2H), 7.03 (td, J =7.7, 1.4 Hz, 1H), 6.86 (dd, J = 8.0, 1.2 Hz, 1H), 6.73 (td, J = 7.6, 1.2Hz, 1H), 6.56 (d, J = 15.5 Hz, 1H), 6.39 (d, J = 16.1 Hz, 1H), 6.18 (dt,J = 15.9, 7.0 Hz, 1H), 4.30 (t, J = 6.9 Hz, 2H), 2.75 (q, J = 6.8 Hz,2H) D12

ES⁺ (M + H)⁺ 378 ¹H NMR (CD₃OD) δ: 7.90 (s, 1H), 7.83 (s, 1H), 7.55 (d,J = 15.7 Hz, 1H), 7.09-7.23 (m, 3H), 7.03 (td, J = 7.7, 1.2 Hz, 1H),6.87 (dd, J = 8.0, 1.4 Hz, 1H), 6.74 (td, J = 7.7, 1.2 Hz, 1H),6.61-6.70 (m, 3H), 6.57 (d, J = 15.8 Hz, 1H), 4.21 (t, J = 6.9 Hz, 2H),3.33 (t, J = 7.1 Hz, 2H), 2.89 (s, 3H), 2.13 (quin, J = 7.1 Hz, 2H) D13

ES⁺ (M + H)⁺ 372 ¹H NMR (CD₃OD) δ: 7.81 (s, 1H), 7.63 (s, 1H), 7.48 (br.d, J = 7.7 Hz, 1H), 7.46 (d, J = 15.7 Hz, 1H), 7.32 (br. d, J = 8.2 Hz,1H), 7.16 (dd, J = 7.9, 1.3 Hz, 1H), 7.08 (m, 3H), 6.88 (s, 1H), 6.86(dd, J = 8.1, 1.4 Hz, 1H), 6.73 (td, J = 7.6, 1.5 Hz, 1H), 6.49 (d, J =15.5 Hz, 1H), 4.42 (t, J = 7.0 Hz, 2H), 3.29 (t, J = 7.0 Hz, 2H) D14

ES⁺ (M + H)⁺ 363 ¹H NMR (CD₃OD) δ: 7.94 (s, 1H), 7.80 (s, 1H), 7.56 (d,J = 15.7 Hz, 1H), 7.12-7.35 (m, 6H), 7.04 (td, J = 7.7, 1.2 Hz, 1H),6.87 (dd, J = 8.1, 1.2 Hz, 1H), 6.74 (td, J = 7.6, 1.4 Hz, 1H), 6.58 (d,J = 15.7 Hz, 1H), 4.48 (s, 2H), 4.34 (t, J = 5.1 Hz, 2H), 3.82 (t, J =5.1 Hz, 2H) D15

ES⁺ (M + H)⁺ 363 ¹H NMR (CD₃OD) δ: 7.96 (s, 1H), 7.83 (s, 1H), 7.62 (d,J = 15.7 Hz, 1H), 7.08-7.37 (m, 6H), 6.81-6.99 (m, 3H), 6.57 (d, J =15.5 Hz, 1H), 4.38 (t, J = 6.7 Hz, 2H), 3.95 (t, J = 5.8 Hz, 2H), 2.32(quin, J = 6.4 Hz, 2H) D16

Method E

Compounds described herein, where n=1, and R1, X, R2, R3, R4, R5 are asdefined anywhere herein, can be prepared by heterocycle ring formationusing methods well known to those skilled in the art, examples of whichcan be found in, for example, Joule J A and Mills K, HeterocyclicChemistry, Fifth Edition, John Wiley & Sons, Inc., Hoboken, N.J., USA.This methodology allows for synthesis of both monocyclic and bicyclicheterocyclic systems. As compared to previous methods described in thisinvention, method 5 consists in building a mono or bicyclic systembearing R1-X and/or C(R4)=C(R5)-CONH(C₆H₂R2R3(NH₂)) or a protected orunprotected synthetic precursor (see schemes above for genericexamples). Thus adequately substituted reagents are coupled to formheterocyclic ring systems using methods such as the Hantsch thiazolesynthesis, the Fisher indole synthesis, the Davidson or Robinson-Gabrieloxazole syntheses, as well as other annulation reactions usingcomplementary bifunctional reagents to effect ring closure andaromatization. Similar techniques can be used to prepare bicyclicheterocycles by expanding monocyclic analogs. For example, azabridgedtriazolothiazoles and triazolooxazoles can be obtained by methodsdescribed in, for example, Pilla M et al, Bioorg Med Chem Lett 20 (2010)7521; pyrazolopyridines can be prepared as detailed in, for example,Riether D et al, J Med Chem 53 (2010) 6681. The synthesis of substitutedindolazines has also been detailed in many articles.

Example 9:(E)-N-(2-aminophenyl)-3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamideE1

(E)-ethyl 3-(2-aminothiazol-5-yl)acrylate

2-Aminothiazole-5-carbaldehyde (0.25 g, 2 mmol) was dissolved inanhydrous THF (20 mL). (Ethoxycarbonylmethylene)triphenylphosphorane(0.790 g, 2.2 mmol) was added at room temperature and the reactionmixture was heated overnight at 65° C. The reaction mixture was thenevaporated under reduced pressure. The residue was purified by silicagel column chromatography using a gradient of 50-80% EtOAc in Hexanes toprovide pure (E)-ethyl 3-(2-aminothiazol-5-yl)acrylate (0.24 g) as awhite solid. ES⁺ (M+H)⁺ 199.

(E)-ethyl 3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylate

1,3-Dichloroacetone (0.252 g, 2 mmol) was added to a solution of(E)-ethyl 3-(2-aminothiazol-5-yl)acrylate (0.199 g, 1 mmol) in EtOH (5mL). The solution was heated at 80° C. overnight in a closed vial. Thereaction mixture was then evaporated and the residue was treated with asaturated NaHCO₃ solution (20 mL). It was extracted with EtOAc (30 mL).The organic layer was separated, dried over Na₂SO₄, filtered andevaporated. The crude was purified by silica gel column chromatography(50-100% gradient of EtOAc in Hexanes) to provide pure (E)-ethyl3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylate (0.080 g) as atan solid. ES⁺ (M+H)⁺ 281.

(E)-3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylic acid

A solution of (E)-ethyl3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylate (0.080 g, 0.28mmol) in EtOH (5 mL) was treated with a 1M aqueous solution of KOH (1mL). The mixture was heated to 50° C. for 6 h. The reaction mixture wasthen evaporated under reduced pressure and water (10 mL) was added tothe residue. This solution was carefully acidified to pH 4 with 3Maqueous HCl. Since the product was soluble in water, the acidifiedsolution was evaporated in vacuo to get(E)-3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylic acid as an HClsalt along with inorganic solids, which was used for the next stepwithout further purification. ES⁺ (M+H)⁺ 253.

(E)-tert-butyl(2-(3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamido)phenyl)carbamate

The crude HCl salt of(E)-3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylic acid (0.080 g,0.28 mmol, based on (E)-ethyl3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylate) was suspended inDCM (10 mL. DIPEA (0.22 g, 1.68 mmol), tert-butyl-2-aminophenylcarbamate(0.087 g, 0.42 mmol) and HATU (0.160 g, 0.42 mmol) were added and thereaction mixture was stirred overnight at room temperature undernitrogen. After completion of the reaction as indicated by HPLC, thereaction mixture was washed with saturated NaHCO₃ and brine. The organiclayer was then dried (Na₂SO₄), filtered and evaporated under reducedpressure. The crude product was purified by silica gel columnchromatography using a gradient of 0 to 8% MeOH in DCM to provide pure(E)-tert-butyl (2-(3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamido)phenyl) carbamate (0.033 g) as a tansolid. ES⁺ (M+Na)⁺ 465.

(E)-N-(2-aminophenyl)-3-(64ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamide

(E)-tert-butyl (2-(3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamido)phenyl) carbamate (0.033 g, 0.071 mmol)was dissolved in dioxane (2 mL). A 4M solution of HCl in dioxane (2. mL)was then added and the mixture stirred at room temperature for 3 h. Saltprecipitation was observed. The reaction mixture was then filtered andwashed with DCM (3 mL). The white solid was treated with a saturatedNaHCO3 solution to neutralize the acid. After washing with water anddrying under vacuum, pure(E)-N-(2-aminophenyl)-3-(6-(ethoxymethyl)imidazo[2,1-b]thiazol-2-yl)acrylamide (14 mg) was obtained as a tan solid. ES⁺(M+H)⁺ 343.

Example 10: (E)-N-(2-aminophenyl)-3-(2-cinnamylthiazol-4-yl)acrylamide,E2

(E)-4-phenylbut-3-enamide

A solution of (E)-4-phenylbut-3-enoic acid (1.5 g, 9.25 mmol) indichloromethane (100 mL) was cooled to 0° C. Oxalyl chloride (1.76 g,13.86 mmol) was then added dropwise. After addition of three drops ofanhydrous DMF, the reaction mixture was brought to room temperature andstirred for 2 h. Dichloromethane was evaporated under vacuum. The cruderesidue was dissolved in toluene (25 mL) and concentrated in-vacuo. Thisoperation was repeated two times to give the acid chloride, which wasdissolved in THF (30 mL) and treated with aqueous ammonium hydroxide(30%) (20 mL) to give the corresponding amide. Purification by silicagel column chromatography using a 20-100% gradient of EtOAc in hexanegave pure (E)-4-phenylbut-3-enamide (1.3 g) as a white solid.

(E)-4-phenylbut-3-enethioamide

Lawesson's reagent (1.88 g, 4.65 mmol) was added to(E)-4-phenylbut-3-enamide (500 mg, 3.10 mmol) in toluene (25 mL). Thereaction mixture was refluxed for 24 h then cooled to room temperature.The solvent was then removed under reduced pressure. The crude residuewas purified twice by column chromatography to give >90% pure(E)-4-phenylbut-3-enethioamide (320 mg).

(E)-3-(2-cinnamylthiazol-4-yl)acrylic acid

(E)-4-phenylbut-3-enethioamide (120 mg, 0.68 mmol) was dissolved inethanol (20 mL). (E)-5-bromo-4-oxopent-2-enoic acid (290 mg, 1.50 mmol)was then added at room temperature and the reaction mixture was stirredfor 1 h. The solution was concentrated and the crude residue waspurified by column chromatography to give(E)-3-(2-cinnamylthiazol-4-yl)acrylic acid (90 mg). ES⁺ (M+H)+272.

[Note: (E)-5-bromo-4-oxopent-2-enoic acid was synthesized fromcommercially available (E)-4-oxopent-2-enoic acid using(2-carboxyethyl)triphenylphosphonium tribromide in THF]

(E)-N-(2-aminophenyl)-3-(2-cinnamylthiazol-4-yl)acrylamide

DIPEA (0.21 g, 0.54 mmol), o-phenylene diamine (39 mg, 0.36 mmol) andHATU (89 mg, 0.23 mmol) were added to a solution of(E)-3-(2-cinnamylthiazol-4-yl)acrylic acid (50 mg, 0.18 mmol) in DCM (20mL) and the reaction mixture was stirred overnight at room temperatureunder nitrogen. After completion of the reaction as indicated by HPLC,the reaction mixture was washed with saturated NaHCO₃ and brine. Theorganic layer was then dried (Na₂SO₄) and evaporated to give the crudeproduct. Repeated silica gel column chromatography using a 0-10%gradient of MeOH, containing 0.1% NH₃ in DCM gave pure(E)-N-(2-aminophenyl)-3-(2-cinnamylthiazol-4-yl)acrylamide (26 mg) as atan-colored solid. ES⁺ (M+H)⁺ 362. ¹H NMR (CD₃OD) δ: 7.66 (s, 1H), 7.60(d, J=15.4 Hz, 1H), 7.39-7.45 (m, 2H), 7.27-7.35 (m, 2H), 7.20 (dd,J=8.0, 1.4 Hz, 1H), 7.17-7.26 (m, 1H), 7.04 (ddd, J=8.0, 7.7, 1.4 Hz,1H), 7.05 (d, J=15.3 Hz, 1H), 6.87 (dd, J=8.0, 1.4 Hz, 1H), 6.74 (td,J=7.7, 1.4 Hz, 1H), 6.66 (dt, J=15.9, 1.1 Hz, 1H), 6.47 (dt, J=15.9, 6.9Hz, 1H), 3.95 (dd, J=6.9, 1.1 Hz, 2H)

Method F

Compounds described herein, where n=0, Cy is a mono or bicyclicheterocyclic amine, can be prepared, amongst other potential approaches,by Wittig or Horner Wadsworth Emmons coupling of an N-protected mono orbicyclic amino heterocyclic ketone with a 4-α-phosphoranylidenemethyl orphosphonate-substituted or unsubstituted 4-alkyl or aralkyl benzoic acidderivative, such as, but not limited to, an ester or amide. Theexocyclic alkene substituted protected heterocyclic amine derivative canbe deprotected by methods well known to those skilled in the art andwhich can be found, for example, in P. G. M. Wuts and T. W. Greene,2006, Greene's Protective Groups in Organic Synthesis, Fourth Edition,John Wiley & Sons, Inc., Hoboken, N.J., USA. The amine can then bederivatized by R1-V substituents using methods as diverse as, but notlimited to, acylation, alkylation, reductive amination. Saponificationof the benzoate ester, if present, allows for reaction of the acid witha protected or unprotected substituted or unsubstitutedo-phenylenediamine. Alternatively, the protected or unprotectedsubstituted or unsubstituted o-phenylenediamine can be introduced at anearlier step in the synthesis. Compounds of the invention,R1-V-Cy-U—Ar/Het-CO—NH—C₆H₂R2R3-NH₂, are obtained after deprotection ofthe amino group using methodologies well known to those skilled in theart. The double bond between Cy and U can also be reduced byhydrogenation to give saturated analogs.

Example 11:4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-N-(2-aminophenyl)-3-chlorobenzamideF5

(2-Chloro-4-(methoxycarbonyl)benzyl)triphenylphosphonium bromide

Methyl 3-chloro-4-methylbenzoate (2.20 g, 11.96 mmol) was dissolved incarbon tetrachloride (30 mL) and N-bromosuccinimide (2.10 g, 11.80 mmol)was added followed by a catalytic amount of benzoyl peroxide (25 mg).The reaction mixture was refluxed for 6 h. (ca. 90% conversion). Aftercooling to room temperature, a precipitate was filtered. The filtratewas concentrated to give crude brominated intermediate (3.20 g), whichwas used for the next step without further purification.

The brominated intermediate from above (3.20 g, 12.17 mmol) wasdissolved in toluene (100 mL) and triphenylphosphine (6.50 g, 12.17mmol) was added. The reaction mixture was heated at 70° C. for 6 h.Precipitation was observed right away. On completion as monitored by TLCthe reaction mixture was cooled to room temperature and diluted withtoluene (100 mL). The precipitate was filtered, washed with hexanes andair dried to give 4.68 g of(2-chloro-4-(methoxycarbonyl)benzyl)triphenylphosphonium bromide as awhite solid. ES⁺ (M+H)⁺ 445.1.

tert-Butyl3-(2-chloro-4-(methoxycarbonyl)benzylidene)azetidine-1-carboxylate

(2-Chloro-4-(methoxycarbonyl)benzyl)triphenylphosphonium bromide (1.04g, 1.98 mmol) was dissolved in N,N-dimethylformamide (DMF, 20 mL) andthe solution was cooled to 0° C. A 60% suspension of NaH in paraffin oil(80 mg, 2.00 mmol) was added and the reaction mixture was stirred at 0°C. for 15 mins. A solution of tert-butyl 3-oxoazetidine-1-carboxylate(0.32 g, 1.87 mmol) in anhydrous DMF (5 mL) was added and the reactionmixture was heated overnight at 65° C. After completion of the reactionas indicated by HPLC/MS, the cooled reaction mixture was diluted withEtOAC (20 mL) and quenched with a saturated NH₄Cl solution (10 mL). Theorganic layer was washed with water (3×20 mL) and brine (15 mL). It wasthen dried over anhydrous Na₂SO₄, filtered and evaporated to get thecrude product. This crude was purified by silica gel columnchromatography using 50-80% EtOAc in Hexanes as eluent to providetert-butyl3-(2-chloro-4-(methoxycarbonyl)benzylidene)azetidine-1-carboxylate (0.27g) as a white solid. ES⁺ (M+Na)⁺ 360.

Methyl 4-(azetidin-3-ylidenemethyl)-3-chlorobenzoate

A 4 M solution of HCl in dioxane (5 mL) was added to a solution oftert-butyl3-(2-chloro-4-(methoxycarbonyl)benzylidene)azetidine-1-carboxylate (0.27g, 0.66 mmol) in dioxane:DCM (1:1 v/v, 10 mL) and the mixture wasstirred at room temperature for 3 h. Salt precipitation was observed.The reaction mixture was diluted with diethyl ether (20 mL). Theprecipitate was filtered, washed with ether and dried overnight to getthe HCl salt of methyl 4-(azetidin-3-ylidenemethyl)-3-chlorobenzoate(0.12 g) as an off-white solid. ES⁺ (M+H)⁺ 238

Methyl4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoate

A solution of the hydrochloride salt of methyl4-(azetidin-3-ylidenemethyl)-3-chlorobenzoate (0.20 g, 0.73 mmol) inTHF:DCM (2:1) (25 mL) was neutralized by addition of triethylamine (0.14mL, 0.88 mmol). After stirring at room temperature for 20 mins,indole-6-carboxaldehyde (0.16 g, 1.00 mmol) and sodiumtriacetoxyborohydride (0.50 g, 2.37 mmol) were added and the reactionmixture was heated at 50° C. overnight. It was then diluted with DCM (50mL) and washed with saturated sodium bicarbonate (3×25 mL) and brine(1×15 mL). The organic layer was separated, dried (Na₂SO₄) and filtered.The filtrate was concentrated under vacuum to give the crude productwhich was purified by silica gel column chromatography using 10-40%EtOAc in hexanes as eluent. Fractions containing the pure product werepooled and evaporated to give 0.3 g of methyl4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoate(0.30 g) as a colorless oil. ES⁺ (M+H)⁺ 367

4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoicacid

A 2 M aqueous solution of KOH (1.5 mL) was added to a solution of methyl4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoate(0.3 g, 0.82 mmol) in MeOH (7 mL) and the mixture was stirred at roomtemperature overnight. The mixture was then evaporated under reducedpressure and water (10 mL) was added to the residue. The solution wascarefully acidified to pH 5 with a 3 M aqueous solution of HCl. Theprecipitated solid was extracted with ethyl acetate. The EtOAc layer waswashed with water (2×10 mL) and brine (1×15 mL). It was dried (Na₂SO₄),filtered, and concentrated in vacuo to give4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoicacid as a white solid (0.26 g). ES⁺ (M+H)⁺ 353.

tert-Butyl(2-(4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzamido)phenyl)carbamate

To a solution of4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzoicacid (0.26 g, 0.74 mmol) in DCM (25 mL) was added DIPEA (0.29 g, 2.22mmol), tert-butyl-2-aminophenylcarbamate (0.27 g, 1.18 mmol) and HATU(0.37 g, 0.96 mmol). The reaction mixture was stirred overnight at roomtemperature under a nitrogen atmosphere. After completion of thereaction as indicated by HPLC, the mixture was washed with saturatedsodium bicarbonate (2×20 mL) and brine (1×15 mL). It was dried (Na₂SO₄),filtered and evaporated to give the crude product which was purified bycolumn chromatography (10% MeOH: 90% DCM). After evaporation of pooledfractions of pure product, tert-butyl(2-(4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzamido)phenyl)carbamate(0.2 g) was isolated as an off-white solid. ES⁺ (M+H)⁺ 543.

4-((1-((1H-Indol-6-yl)methyl)azetidin-3-ylidene)methyl)-N-(2-aminophenyl)-3-chlorobenzamide

A 4 M solution of HCl in dioxane (5 mL) was added to a solution oftert-butyl(2-(4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-3-chlorobenzamido)phenyl)carbamate(0.20 g, 0.37 mmol) in dioxane (5 mL) and the mixture was stirred atroom temperature for 3 h. Salt precipitation was observed. Aftercompletion of the reaction as indicated by HPLC/MS, the mixture wasdiluted with diethyl ether (20 mL) and the salt was filtered to give 110mg of ca. 85% pure product. 45 mg were purified by mass-triggeredreverse phase auto-purification (0.1% NH₄OH as additive) to give 8 mg ofpure4-((1-((1H-indol-6-yl)methyl)azetidin-3-ylidene)methyl)-N-(2-aminophenyl)-3-chlorobenzamide.¹H ¹H NMR (CD₃OD) δ: 8.03 (d, J=1.8 Hz, 1H), 7.85 (dd, J=8.2, 1.8 Hz,1H), 7.52 (d, J=8.1 Hz, 1H), 7.38 (s, 1H), 7.30 (d, J=8.2 Hz, 1H), 7.22(d, J=3.2 Hz, 1H), 7.16 (dd, J=7.8, 1.3 Hz, 1H), 7.07 (ddd, J=8.1, 7.3,1.5 Hz, 1H), 7.02 (dd, J=8.1, 1.5 Hz, 1H), 6.89 (dd, J=8.1, 1.4 Hz, 1H),6.76 (td, J=7.7, 1.4 Hz, 1H), 6.68 (quin, J=2.3 Hz, 1H), 6.41 (dd,J=3.2, 1.0 Hz, 1H), 4.23-4.34 (m, 2H), 4.10-4.19 (m, 2H), 3.93 (s, 2H);ES⁺ (M+H)⁺ 443.

Com- pound Structure R—X or aldehyde F1 

F2 

F3 

F4 

F5 

F6 

F7 

F8 

N/A F9 

N/A F10

F11

N/A F12

F13

F14

F15

F16

F17

F18

F19

F20

Com- pound diamine MS NMR F1 

ES⁺ (M + H)⁺ 442 ¹H NMR (CD₃OD) δ: 8.02 (d, J = 8.2 Hz, 1H), 7.21-7.52(m, 10H), 6.85-7.15 (m, 2H), 6.50 (s, 1H), 5.14 (s, 2H), 3.44-3.71 (m,4H), 2.32-2.61 (m, 4H) F2 

ES⁺ (M + H)⁺ 399 ¹H NMR (CD₃OD) δ: 8.52 (d, J = 1.8 Hz, 1H), 8.45 (dd, J= 4.9, 1.6 Hz, 1H), 7.93 (d, J = 8.1 Hz, 2H), 7.86 (dt, J = 7.8, 1.9 Hz,1H), 7.42 (ddd, J = 7.8, 4.9, 0.7 Hz, 1H), 7.33 (d, J = 8.1 Hz, 2H),7.18 (dd, J = 7.8, 1.3 Hz, 1H), 7.07 (ddd, J = 8.0, 7.3, 1.4 Hz, 1H),6.90 (dd, J = 8.1, 1.2 Hz, 1H), 6.76 (td, J = 7.6, 1.4 Hz, 1H), 6.39 (s,1H), 3.60 (s, 2H), 2.40-2.65 (m, 8H) F3 

ES⁺ (M + H)⁺ 409 ¹H NMR (CD₃OD) δ: 7.92 (d, J = 8.0 Hz, 2H), 7.53 (d, J= 8.4 Hz, 1H), 7.33-7.43 (br. s, 1H), 7.24 (d, J = 8.0 Hz, 2H), 7.22 (d,J = 3.2 Hz, 1H), 7.17 (dd, J = 7.6, 1.5 Hz, 1H), 7.07 (td, J = 7.9, 1.5Hz, 1H), 7.03 (dd, J = 8.5, 1.5 Hz, 3H), 6.89 (dd, J = 8.0, 1.3 Hz, 1H),6.76 (td, J = 7.7, 1.4 Hz, 1H), 6.42 (dd, J = 3.2, 0.9 Hz, 1H), 6.34(quin, J = 1.8 Hz, 1H), 4.36 (br. s., 2H), 4.17 (br. s., 2H), 3.95 (s,2H) F4 

ES⁺ (M + H)⁺ 411 ¹H NMR (CD₃OD) δ: 7.91 (d, J = 8.0 Hz, 2H), 7.55 (d, J= 8.2 Hz, 1H), 7.39 (br. s., 1H), 7.32 (d, J = 8.0 Hz, 2H), 7.26 (t, J =1.6 Hz, 1H), 7.17 (d, J = 8.2 Hz, 1H), 7.07 (td, J = 8.0, 1.4 Hz, 1H),7.00 (dd, J = 8.2, 1.4 Hz, 1H), 6.90 (dd, J = 8.0, 1.4 Hz, 1H), 6.76(td, J = 7.0, 1.9 Hz, 1H), 6.44 (d, J = 3.3 Hz, 1H), 4.02 (s, 2H), 3.73(m, 2H), 3.36-3.52 (m, 2H), 2.87-3.03 (m, 3H) F5 

ES⁺ (M + H)⁺ 443 ¹H NMR (CD₃OD) δ: 8.03 (d, J = 1.8 Hz, 1H), 7.85 (dd, J= 8.2, 1.8 Hz, 1H), 7.52 (d, J = 8.1 Hz, 1H), 7.38 (s, 1H), 7.30 (d, J =8.2 Hz, 1H), 7.22 (d, J = 3.2 Hz, 1H), 7.16 (dd, J = 7.8, 1.3 Hz, 1H),7.07 (ddd, J = 8.1, 7.3, 1.5 Hz, 1H), 7.02 (dd, J = 8.1, 1.5 Hz, 1H),6.89 (dd, J = 8.1, 1.4 Hz, 1H), 6.76 (td, J = 7.7, 1.4 Hz, 1H), 6.68(quin, J = 2.3 Hz, 1H), 6.41 (dd, J = 3.2, 1.0 Hz, 1H), 4.29 (q, J = 1.9Hz, 2H), 4.16 (t, J = 1.9 Hz, 2H), 3.93 (s, 2H) F6 

ES⁺ (M + H)⁺ 406 ¹H NMR (CD₃OD) δ: 8.56 (dd, J = 2.2, 0.7 Hz, 1H), 8.48(dd, J = 4.8, 1.5 Hz, 1H), 8.04 (d, J = 1.6 Hz, 1H), 7.82-7.91 (m, 2H),7.45 (ddd, J = 7.7, 4.9, 0.8 Hz, 1H), 7.30 (d, J = 8.2 Hz, 1H), 7.16(dd, J = 8.0, 1.4 Hz, 1H), 7.08 (ddd, J = 8.1, 7.3, 1.5 Hz, 1H), 6.89(dd, J = 8.1, 1.2 Hz, 1H), 6.76 (td, J = 7.6, 1.5 Hz, 1H), 6.70 (quin, J= 2.0 Hz, 1H), 4.31-4.41 (m, 2H), 4.17-4.27 (m, 2H), 3.95 (s, 2H) F7 

ES⁺ (M + H)⁺ 433 ¹H NMR (CD₃OD) δ: 8.53 (d, J = 1.9 Hz, 1H), 8.45 (dd, J= 4.9, 1.4 Hz, 1H), 8.04 (br. s, 1H), 7.87 (d, J = 8.0 Hz, 1H), 7.86 (d,J = 8.3 Hz, 1H), 7.43 (dd, J = 8.3, 4.9 Hz, 1H), 7.39 (d, J = 8.0 Hz,1H), 7.18 (d, J = 8.0 Hz, 1H), 7.08 (t, J = 7.4 Hz, 1H), 6.90 (d, J =8.0 Hz, 1H), 6.76 (t, J = 7.7 Hz, 1H), 6.37 (s, 1H), 3.62 (s, 2H), 2.62(t, J = 5.5 Hz, 2H), 2.46-2.55 (m, 4H), 2.43 (t, J = 5.5 Hz, 2H) F8 

ES⁺ (M + H)⁺ 382, 384 ¹H NMR (CD₃OD) δ: 8.17 (s, 1H), 8.02 (dd, J = 8.4Hz, 1H), 7.48 (br. m, 4H), 7.43 (dd, J = 8.4 Hz, 1H), 6.74 (br. s, 1H),4.06 (br., 1H), 3.92 (br. , 1H), 3.15-3.0 (m, 2H), 2.84 (s, 3H), 2.8-2.5(m., 2H), 2.30 (br. m, 2H), 2.05 (dd, 1H), 1.70 (dd, 1H) F9 

ES⁺ (M + H)⁺ 299 ¹H NMR (DMSO-d₆) δ: 9.50 (s, 1H), 7.70 (t, 1H), 7.30(d, 1H), 7.1-6.9 (3 m, 3H), 6.75 (d, 1H), 6.58 (t, 1H), 6.30 (br. s,1H), 5.55 (br. m, 2H), 5.35 (br. m, 2H), 4.95 (br. s, 2H) F10

ES⁺ (M + H)⁺ 369 ¹H NMR (CD₃OD) δ: 8.21 (s, 1H), 8.02 (d, J = 8.4 Hz,1H), 7.43 (br. s, 1H), 7.42 (d, J = 8.4 Hz, 1H), 7.27 (br. m, 3H), 6.82(br. s, 1H), 5.18 (br. s, 2H), 4.94 (2 d, AB system, 2H), 3.19 (br. m,2H), 1.05 (br. m, 1H), 0.56 (br. d, J = 7.8 Hz, 2H), 0.41 (br. m, 2H)F11

ES⁺ (M + H)⁺ 315, 317 ¹H NMR (DMSO-d₆) δ: 9.72 (s, 1H), 8.08 (s, 1H),7.87 (d, J = 8.1 Hz, 1H), 7.15 (d, J = 8.4 Hz, 1H), 7.11 (d, J = 7.8 Hz,1H), 6.96 (ddd, J = 7, 7, 1.5 Hz, 1H), 6.74 (dd, J = 8, 8, 1.2, 1H),6.60-6.53 (2 m, 2H), 5.51 (br. m, 2H), 5.33 (br. m, 2H), 4.93 (s, 2H)F12

ES⁺ (M + H)⁺ 334 ¹H NMR (CD₃OD) δ: 8.09 (d, J = 8.4 Hz, 2H), 7.48 (br.m, 4H), 7.38 (d, J = 8.4 Hz, 2H), 6.65 (br. m, 1H), 5.30 (dd, 2H), 5.05(dd, 2H), 4.95 (br. m, 2H), 1.12 (br. m, 1H), 0.74 (br. m, 2H), 0.47(br. m, 2H) F13

ES⁺ (M + H)⁺ 362 ¹H NMR (CD₃OD) δ: 8.08 (d, J = 8.4 Hz, 2H), 7.50 (br.m, 4H), 7.45 (d, J = 8.4 Hz, 2H), 6.65 (br. s, 1H), 3.77 (m, 2H),3.2-2.9 (br. m, 4H), 2.9-2.5 (br. m, 4H), 1.17 (m, 1H), 0.79 (m, 2H),0.47 (m, 2H) F14

ES⁺ (M + H)⁺ 378 ¹H NMR (CD₃OD) δ: 8.08 (d, J = 8.4 Hz, 2H), 7.51 (br.m, 4H), 7.44 (d, J = 8.4 Hz, 2H), 6.65 (br. s, 1H), 3.72-3.56 (br. m,2H), 3.3-3.1 (br. m, 2H), 3.05-2.7 (br. m, 6H), 1.17 (s, 9H) F15

ES⁺ (M + H)⁺ 380 F16

ES⁺ (M + H)⁺ 385 ¹H NMR (CD₃OD) δ: 8.10 (d, J = 8.4 Hz, 2H), 8.0 (br. m,1H), 7.51 (br. m, 7H), 7.39 (d, J = 8.4 Hz, 2H), 6.67 (br. m, 1H), 5.39(br. s, 2H), 5.14 (br. s, 2H), 4.9 (br. under solvent peak), 2.67 (br.s, 3H) F17

ES⁺ (M + H)⁺ 370 ¹H NMR (CD₃OD) δ: 8.09 (d, J = 8.4 Hz, 2H), 7.51 (br.m, 9H), 7.37 (d, J = 8.4 Hz, 2H), 6.66 (br. m, 1H), 5.24 (m, AB system,2H), 4.95 (m, under solvent peak), 4.59 (s, 2H) F18

ES⁺ (M + H)⁺ 371 F19

ES⁺ (M + H)⁺ 352 ¹H NMR (CD₃OD) δ: 8.09 (d, J = 8.4 Hz, 2H), 7.48 (br.m, 4H), 7.37 (d, J = 8.4 Hz, 2H), 6.61 (br. m, 1H), 5.35 (br. m, 2H),5.05 (m, under solvent peak), 3.44 (s, 2H), 1.33 (s, 2H) F20

ES⁺ (M + H)⁺ 352 ¹H NMR (CD₃OD) δ: 8.08 (d, J = 8.4 Hz, 2H), 7.46 (m,1H), 7.38 (d, J = 8.4 Hz, 2H), 7.22 (m, 2H), 6.64 (br. m, 1H), 5.31 (m,2H), 5.09 (m, 2H), 3.30 (m, 2H), 1.13 (m, 1H), 0.73 (m, 2H), 0.47 (m,2H)Method G

Compounds described herein, where n=1, and R1, X, R2, R3, R4, R5, andAr/Het are defined as defined anywhere herein, can be prepared bycross-coupling reactions well known to those skilled in the art such asthe Mizoroki-Heck reaction, the Suzuki-Miyaura coupling, the Negishicoupling, and other such methods as described in, for example, Alonso DA and Najera C, Science of Synthesis, 47 (2010), 439-482 and presentedin the generic scheme above, where react, (i=5-8) are reactive moietiesselected as appropriate for the different coupling strategies mentionedabove, and where P and P′ are adequate protecting groups that can beintroduced using methods well known to those skilled in the art andwhich are described for example in P. G. M. Wuts and T. W. Greene, 2006,Greene's Protective Groups in Organic Synthesis, Fourth Edition, JohnWiley & Sons, Inc., Hoboken, N.J., USA. For example, one can preparecompounds of the invention using the Mizoroki-Heck reaction of a mono orbicyclic halogenated heterocycle, or a mono or bicyclic heterocycletriflate (react₅=halogen, OTf, where Tf stands fortrifuloromethylsulfonyl or triflyl), which can be prepared by methodswell known to those skilled in the art and detailed in, for example,Joule J A and Mills K, Heterocyclic Chemistry, Fifth Edition, John Wiley& Sons, Inc., Hoboken, N.J., USA, with an activated alkene, i.e.substituted or unsubstituted acrylic ester (react₆=H), to give thecorresponding γ-(heterocycle)acrylate ester Ar/Het-CR4=CR5-COOR7, usingprotecting groups on the heterocycle when necessary. The R1-X moiety canthen be added to this intermediate by synthetic methods well known tothose skilled in the art, including but not limited to Heck coupling,Suzuki reaction, alkylation, acylation. Alternatively the R1-Xsubstituent can be coupled to the mono or bicyclic heterocycle prior tothe Heck reaction to give the same intermediate ester. In all cases theR1-X moiety can be built onto the scaffold in several steps usingsynthetic chemistry methodologies well known to those skilled in theart. The ester can then be hydrolyzed and the acid reacted with aprotected or unprotected substituted or unsubstituted o-phenylenediamineto give compounds of the invention after deprotection if required usingmethods well known to those skilled in the art and which are describedfor example in P. G. M. Wuts and T. W. Greene, 2006, Greene's ProtectiveGroups in Organic Synthesis, Fourth Edition, John Wiley & Sons, Inc.,Hoboken, N.J., USA. Alternatively, the ester of the intermediateprotected or unprotected γ-(heterocycle)acrylate esterAr/Het-CR4=CR5-COOR7 described above could be hydrolyzed and the acidreacted with a protected or unprotected substituted or unsubstitutedo-phenylenediamine to give compounds of the invention after deprotectionif required using methods well known to those skilled in the art.Finally, the Heck coupling of the protected or unprotected halogenatedmono or bicyclic heterocycle or mono or bicyclic heterocycle triflatecould be performed using a substituted or unsubstituted acrylamideprepared by reaction of the corresponding substituted or unsubstitutedacrylic acid, prepared by methods well known to those skilled in theart, with a protected substituted or unsubstituted o-phenylenediamine.The R1-X moiety can then be added to the intermediate amideAr/Het-CR4=CR5-CONH(o-N(R8R9)C₆H₂R2R3), after deprotection of Ar/Hetwhen required, by synthetic methods well known to those skilled in theart, including but not limited to Heck coupling, Suzuki reaction,alkylation, acylation. Alternatively the R1-X substituent can be coupledto the mono or bicyclic heterocycle prior to the Heck reaction. Asmentioned above, the R1-X moiety can be built onto the molecule inseveral steps using synthetic chemistry methodologies well known tothose skilled in the art and which can include, but are not limited to,oxidation, reduction, coupling, protection, and deprotection. Compoundsof the invention can be obtained by deprotection of the ortho-amine onthe amide using methods well known to those skilled in the art.

Example 12:(E)-N-(2-aminophenyl)-3-(1-((1-methylpiperidin-4-yl)methyl)-1H-pyrazol-4-yl)acrylamideG1

1-(4-iodo-1H-pyrazol-1-yl)ethanone

Acetyl chloride (38.2 mL, 1.07 equiv) and triethylamine (86 mL, 1.2equiv) were added at 0° C. to a solution of 4-iodo-1H-pyrazole (100 g,0.515 mol) in dichloromethane (1 L). The mixture was stirred overnightat room temperature. The reaction mixture was poured into water. Theaqueous layer was extracted with dichloromethane. The combined organiclayers were washed with brine, dried over anhydrous sodium sulfate(Na₂SO₄), and filtered. The residue obtained by concentration waspurified by silica gel column chromatography (Hexane/EtOAc 20:1 to 1:1)to give N-acetyl 4-iodo-1H-pyrazole as a solid (110 g, 91%).

(E)-methyl 3-(1-acetyl-1H-pyrazol-4-yl)acrylate

A 5-L multineck flask was fitted with a mechanical stirrer, a gas inletadapter, and a thermometer and cooled in a salt-ice bath to between −10and −15° C. The system was purged with dry nitrogen for a few minutes. Asolution of 1-(4-iodo-1H-pyrazol-1-yl)ethanone (100 g, 0.425 mol) 1.2 Lof N,N-dimethylformamide (DMF) was added followed by methyl acrylate(110 g, 1.275 mol), triethylamine (64 mL, 0.458 mol), trimethylphosphite (5.27 g, 42.5 mmol), and palladium acetate (4.76 g, 21.25mmol). The mixture was then warmed to 110° C. under dry nitrogenatmosphere and stirred for 1 hour. LC/MS analysis of an aliquot showedonly 10% product formation. Trimethyl phosphite (5.27 g, 42.5 mmol), andpalladium acetate (4.76 g, 21.25 mmol) were then added to the reactionmixture. The reaction went to completion after another 1.5 h asmonitored by LC/MS. The mixture was allowed to cool to room temperatureand the DMF was removed under reduced pressure. The residue was stirredwith 1.5 L of methylene chloride, and the suspension was filteredthrough a plug of silica gel. The filtrate was collected and washed with1 L of 3% hydrochloric acid, 1 L of water, and 1 L of saturated brine.The solution was dried over magnesium sulfate and filtered. The solventwas removed under reduced pressure and the residue was purified bysilica gel column chromatography (Hexane/EtOAc 10:1 to 1:1) to give(E)-methyl 3-(1-acetyl-1H-pyrazol-4-yl)acrylate as a solid (70 g, 84%).

(E)-methyl 3-(1H-pyrazol-4-yl)acrylate

Sodium hydrogenocarbonate, NaHCO₃ (32 g, 1.15 equiv), was added to asuspension of protected compound, (E)-methyl3-(1-acetyl-1H-pyrazol-4-yl)acrylate (65 g, 0.33 mol), in MeOH (600 mL).The mixture was stirred for 7 h at room temperature. The solids werethen filtered and washed with dichloromethane. The filtrate wasconcentrated under reduced pressure and the residue was purified bysilica gel column chromatography (Hexane/EtOAc 8:1 to 1:2) to give thetitle compound as a solid (47 g, 92%).

(E)-methyl 3-(14(1-methylpiperidin-4-yl)methyl)-1H-pyrazol-4-yl)acrylate

Triphenylphosphine (393 mg, 1.5 mmol) and (E)-methyl3-(1H-pyrazol-4-yl)acrylate, prepared as described above, (12 mg, 1mmol) were added to a solution of N-methyl-4-hydroxymethyl-piperidine(165 mg, 1.25 mmol) in tetrahydrofuran (THF, 2 mL). After addition ofdi-tert-butyl azodicarboxylate (345 mg, 1.5 mmol), the reaction wasstirred overnight at room temperature. Solvents were evaporated underreduced pressure and the residue was purified by silica gelchromatography using a gradient of Hexane in EtOAc from 1:1 to 0:100v/v. Fractions containing product were pooled and evaporated to give 220mg of pure material (0.84 mmol, 84%).

(E)-3-(14(1-methylpiperidin-4-yl)methyl)-1H-pyrazol-4-yl)acrylic acid

An aqueous 3N sodium hydroxide solution (2 mL) was added to a solutionof (E)-methyl3-(1-((1-methylpiperidin-4-yl)methyl)-1H-pyrazol-4-yl)acrylate (220 mg)in MeOH (5 mL) and THF (3 mL) was added aq NaOH (3N, 2 mL) to saponifythe methyl ester. Workup was performed as described in Example 12 togenerate 209 mg of pure product (0.84 mmol, 100%).

(E)-N-(2-aminophenyl)-3-(1-((1-methylpiperidin-4-yl)methyl)-1H-pyrazol-4-yl)acrylamideG1

A solution of the acrylic acid prepared above (130 mg, 0.52 mmol) in DMF(2 mL) was treated with tert-butyl-(2-aminophenyl)carbamate (114 mg,0.55 mmol), HATU (262 mg, 1.2 eq), and diisopropylethylamine (DIPEA,0.34 mL) at 0° C. The solution was allowed to warm up. After stirring 16h at room temperature, the reaction mixture was quenched with aqueousammonium chloride. The mixture was diluted with water, extracted withdichloromethane. The organic phase was washed with saturated NaHCO₃, andbrine. It was dried over Na₂SO₄, filtered, and concentrated. The residuewas purified by preparative HPLC to afford pure tert-butyloxycarbonyl G1(56 mg, 0.13 mmol, 25%).

Deprotection of the amino group was achieved as described above byovernight treatment of a solution in dioxane (1 mL) and MeOH (1 mL) with4 M HCl in dioxane (0.5 mL). Purification by preparative HPLC gavecompound G1 as a HCl salt. This product was neutralized with a solutionof NaHCO₃ and repurified by preparative HPLC to give pure G1 (18 mg,0.053 mmol, 41%).

¹H NMR (CD₃OD) δ: 7.97 (s, 1H), 7.84 (s, 1H), 7.55 (d, J=15.6 Hz, 1H),7.17 (dd, J=8.0, 4.5 Hz, 1H), 7.05 (dt, 1H), 6.88 (dd, J=8.0, 4.5 Hz,1H), 6.75 (dt, 1H), 6.60 (d, J=15.6 Hz, 1H), 4.14 (d, J=6.6 Hz, 2H),3.6-3.4 (br, 2H), 3.1-2.9 (br, 2H), 2.84 (s, 3H); 2.22 (br, 1H),1.95-1.80 (br, 2H), 1.7-1.45 (br, 2H); ES⁺ (M+H)⁺ 340.

Example 13:(E)-N-(2-aminophenyl)-3-(1-cinnamyl-3,5-dimethyl-1H-pyrazol-4-yl)acrylamideG2

(E)-methyl 3-(3,5-dimethyl-1H-pyrazol-4-yl)acrylate

The preparation of the dimethylpyrazolyl acrylate was performed using asimilar protocol as described for the synthesis of (E)-methyl3-(1H-pyrazol-4-yl)acrylate (example 12). Thus, from 1.1 g of4-iodo-3,5-dimethyl-1H-pyrazole (5 mmol), 440 mg of (E)-methyl3-(3,5-dimethyl-1H-pyrazol-4-yl)acrylate were isolated (2.44 mmol, 49%over 3 steps).

(E)-methyl 3-(1-cinnamyl-3,5-dimethyl-1H-pyrazol-4-yl)acrylate

(E)-methyl 3-(3,5-dimethyl-1H-pyrazol-4-yl)acrylate (360 mg, 2 mmol) wasdissolved in DMF (6 mL). Sodium hydride, (NaH 60% dispersion, 80 mg, 1equiv) was added in small portions while maintaining the temperature at0° C. The mixture was then stirred at room temperature for 1 h. Themixture was cooled to 0° C. and cinnamyl bromide (394 mg, 1 equiv) wasadded. The mixture was then stirred overnight at room temperature. Itwas quenched with aqueous ammonium chloride, diluted with water, andextracted with EtOAc. The combined organic layers were dried overNa₂SO₄, filtered, and concentrated. The residue was purified by columnchromatography using a gradient of hexane/EtOAc (10:1 to 0:100 v/v).Fractions containing pure product were combined and the solvents wereremoved under reduced pressure to yield (E)-methyl3-(1-cinnamyl-3,5-dimethyl-1H-pyrazol-4-yl)acrylate (401 mg, 68%).

(E)-3-(1-cinnamyl-3,5-dimethyl-1H-pyrazol-4-yl)acrylic acid

The acid was obtained as described above in examples 12 and 13. Thus 44mg of pure acid (0.16 mmol) were obtained by base hydrolysis of 124 mg(0.42 mmol) for a yield of 38%.

(E)-N-(2-aminophenyl)-3-(1-cinnamyl-3,5-dimethyl-1H-pyrazol-4-yl)acrylamideG2

Title compound G2 was obtained in two steps as described above bycoupling of the acid (44 mg, 0.16 mmol) with tert-butyl (2-aminophenyl)carbamate followed by acid deprotection. Purification by preparativeHPLC of the neutralized hydrochloride salt gave pure G2 (25 mg, 0.065mmol, 42%).

¹H NMR (CD₃OD) δ: 7.65 (d, J=15.6 Hz, 1H), 7.38 (br d, J=8.4 Hz, 2H),7.29 (br dt, J=8.4, 1.5 Hz, 2H), 7.25-7.23 (m, 1H), 7.17 (dd, J=8.0, 4.5Hz, 1H), 7.04 (dt, J=7.8, 1.5 Hz, 1H), 6.88 (dd, J=7.8, 1.5 Hz, 1H),6.75 (dt, J=7.8, 1.5 Hz, 1H), 6.53 (d, J=15.6 Hz, 1H), 6.4-6.3 (2multiplets, 2H), 4.80 (d, J=4.2 Hz, 2H), 2.43 (s, 3H), 2.41 (s, 3H); ES⁺(M+H)⁺ 373.

Com- pound Structure coupling G1

G2

G3 = D10

G4 = D2

Com- pound R1—X—Y-react₈ MS NMR G1

ES⁺ (M + H)⁺ 340 ¹H NMR (CD₃OD) δ: 7.97 (s, 1H), 7.84 (s, 1H), 7.55 (d,J = 15.6 Hz, 1H), 7.17 (dd, J = 8.0, 4.5 Hz, 1H), 7.05 (dt, 1H), 6.88(dd, J = 8.0, 4.5 Hz, 1H), 6.75 (dt, 1H), 6.60 (d, J = 15.6 Hz, 1H),4.14 (d, J = 6.6 Hz, 2H), 3.6-3.4 (br, 2H), 3.1-2.9 (br, 2H), 2.84 (s,3H); 2.22 (br, 1H), 1.95-1.80 (br, 2H), 1.7- 1.45 (br, 2H) G2

ES⁺ (M + H)⁺ 373 ¹H NMR (CD₃OD) δ: 7.65 (d, J = 15.6 Hz, 1H), 7.38 (brd, J = 8.4 Hz, 2H), 7.29 (br dt, J = 8.4, 1.5 Hz, 2H), 7.25-7.23 (m,1H), 7.17 (dd, J = 8.0, 4.5 Hz, 1H), 7.04 (dt, J = 7.8, 1.5 Hz, 1H),6.88 (dd, J = 7.8, 1.5 Hz, 1H), 6.75 (dt, J = 7.8, 1.5 Hz, 1H), 6.53 (d,J = 15.6 Hz, 1H), 6.4-6.3 (2 multiplets, 2H), 4.80 (d, J = 4.2 Hz, 2H),2.43 (s, 3H), 2.41 (s, 3H) G3 = D10

ES⁺ (M + H)⁺ 369 1H NMR (CD₃OD) - HCl salt - δ: 7.94 (s, 1H), 7.83 (s,1H), 7.67 (d, J = 15.6 Hz, 1H), 7.56-7.42 (m, 8H), 7.41-7.36 (m, 1H),6.63 (d, J = 15.6 Hz, 1H), 4.90 (t, J = 13.5 Hz, 2H) G4 = D2

ES⁺ (M + H)⁺ 363 1H NMR (CD₃OD) - HCl salt - δ: 8.08 (s, 1H), 7.90 (s,1H), 7.71 (d, J = 15.5 Hz, 1H), 7.37-7.46 (m, 2H), 7.21-7.37 (m, 4H),6.63 (d, J = 15.7 Hz, 1H), 6.56-6.71 (m, 1H), 6.43 (dt, J = 15.8, 6.2Hz, 1H), 4.96 (dd, J = 6.3, 1.1 Hz, 2H)MethodsHDAC Enzyme Inhibition

The HDAC activity inhibition assay was performed as follows to determinethe ability of a test compound to inhibit HDAC enzymatic activity.Serial dilutions of HDAC inhibitors were prepared in HDAC assay buffer(25 mM Tris/HCl, pH 8.0, 137 mM NaCl, 2.7 mM KCl, 1 mM MgCl₂, pH 8) in96-well assay plates (Fisher scientific, #07-200-309) and werepre-incubated for 2 hours at room temperature in the presence of 1254μg/ml BSA and purified HDAC1 (BPS Bioscience, San Diego, Calif.,#50051), HDAC2 (BPS Bioscience, #50053), or HDAC3/NcoR2 (BPS Bioscience,#50003) at concentrations of 1.25, 1.32, and 0.167 vg/mL, respectively.Following pre-incubation, Fluor-de-Lys™ substrate (Enzo Life Sciences,Plymouth Meeting, Pa., BML-KI104-0050) was added to a finalconcentration of 10 μM and plates were further incubated for 30 minutesat room temperature. The enzymatic reaction was stopped by addition ofTrichostatin A (Sigma-Aldrich, St Louis, Mo., #T8552, finalconcentration: 100 nM) and trypsin (MP Biomedicals, Solon, Ohio,#02101179) was added to reach a final concentration of 100 μg/mL. Aftera 15 minute incubation at room temperature, fluorescence was recordedusing a Spectramax M2 fluorometer (Molecular Devices, Sunnyvale, Calif.)with excitation at 365 nm and emission at 460 nm. IC50 values werecalculated by using a sigmoidal dose-response (variable slope) equationin GraphPad Prism® 5 for Windows (GraphPad Software, La Jolla, Calif.).Results for selected compounds of the invention in the HDAC activityinhibition assay are presented in Tables 1 and 4 (IC50 ranges: IA>2004,A<1 μM, 1<B<5 μM, 5<C<10 μM, 10<D<20 μM, ND: not determined)

TABLE 1 IC50 for inhibition of HDAC1, 2, and 3 isoforms compound HDAC1HDAC2 HDAC3 D1 A A A D2 B B A D3 A A A D9 A A A B6 A A A B2 A B A B4 A BA B3 A A A D16 B B A B5 A A A A12 B C A D4 A B A D7 A B A D8 A A A D14 AA A D11 A A A D5 A B A D12 A A A D13 A A A D15 A A A D10 A B A D6 B B AA6 C C A A8 A B A A9 B B A A10 B B A E1 B C A A2 C D A A7 B B A C2 IA IAB C3 B B A A11 B B A C1 B B A B1 B C A A1 B C A A3 C C A A4 IA IA B A5 DD A E2 A B A F1 A B A F2 A A A F3 A A A F4 A ND A F5 A B A F6 A B A F7 AA A G1 B B A G2 B B AAcid Stability Determination

A 100 μM solution of test compound was prepared by dilution of a 10 mMDMSO stock solution in a 0.01 M solution of HCl in deionized water.Immediately after mixing, an aliquot (100 μL) was sampled and analyzedby HPLC/UV. The area under the compound peak was determined and used asthe time zero reference point. The remainder of the acid sample wasincubated at 50° C. and samples were taken after 2, 4, and 24 hours ofincubation. On a few occasions, samples were taken at 30 rather than 24hours. These were analyzed by the same HPLC/UV method and the area ofthe peak corresponding to the test compound was measured. Percentremaining at a given time point was then calculated as the ratio of thearea under the peak after incubation to that at time zero times 100. Inthose cases where a 30 hour time point was recorded, the percentremaining at 24 hours was obtained by interpolation of the percentremaining versus time curve assuming a unimolecular process, i.e. amonoexponential decay. Percent remaining after 24 hours incubation arepresented in Tables 2 and 4 below, where A corresponds to more than 60%,B is between 40 and 60%, C covers 20 to 40% and D means less than 20%.

Brain Penetration Studies

Test compounds were prepared at either 0.5 mg/ml or 5 mg/ml in 30%hydroxypropyl-β-cyclodextrin, 100 mM sodium acetate pH 5.5, 5% DMSO.C57/BL6/J mice were dosed s.c. at 5 mg/kg or 50 mg/kg, or i.v. at 5mg/kg. Animals were euthanized at pre-dose, 5, 15, 30 min, 1, 2 and 4hours post-dose and plasma and brain obtained. Three animals per doseper time points were used. The levels of compound in the plasma andbrain were determined by standard LC/MS/MS methods. Brain/plasma ratio(BPR) was calculated as the ratio of the C_(max)(brain)/C_(max)(plasma).The results are shown in Tables 2 and 4, where IA corresponds to a BPRless than 0.1, D is between 0.1 and 0.2, C is 0.2 to 0.5, B comprises0.5 to 1 and A is greater than 1.

In-Cell Deacetylase Inhibition Assay (DAC Assay)

GM 15850(lymphoblastoid cells line) cells were seeded in 96-well platesat an appropriate density (100,000 cells/well) in 90 μL RPMI1640 mediumcontaining 10% v/v fetal bovine serum (FBS), 1% v/vpenicillin/streptomycin, and 1% v/v L-glutamine. Compound dilutions weremade in 100% DMSO followed by parallel dilution in media with 2% DMSO.10 μl of the compound dilutions were added to the cells to achieve thedesired concentrations. The final concentration of DMSO in each well was0.2%. The cells were incubated for 4 h at 37° C. with 5% CO₂. Afterincubation, the cells were centrifuged down and the supernatant wasremoved. The cell pellets were washed with 100 μL phosphate-bufferedsaline (PBS) and then lysed with 45 μL lysis buffer (HDAC assay bufferat pH 8.0 (25 mM Tris/HCl, 137 mM NaCl, 2.7 mM KCl, 1 mM MgCl₂)+1% v/vIgepal CA-630). To initiate the reaction, the HDAC substrate KI-104(Enzo Life Sciences, Farmingdale, N.Y.) was added to a finalconcentration of 50 μM. The reaction was stopped after 30 min incubationby addition of 50 μL developer (6 mg/mL trypsin in HDAC assay buffer).The reaction was allowed to develop for 30 min at room temperature andthe fluorescence signal was detected using a fluorometer (Spectramax M2,Molecular Devices, Sunnyvale, Calif.) with excitation and emissionwavelengths of 360 nm and 470 nm respectively. The data was fitted to asigmoidal dose response equation with variable slope in GraphPad Prism5.0 (GraphPad Software, La Jolla, Calif.) to determine IC50. Bottom andtop of the curve were fixed to the average fluorescence response ofcontrol wells with no cells and cells but no compound respectively.IC50's are reported in Table 2 and 4, where A stands for IC50 less than1 μM, B between 1 and 5 μM, C from 5 to 10 μM, D from 10 to 20 μM, andIA for IC50 above 20 μM.

Cell Proliferation Assay

HCT116 cells (5000 cells/well) in 80 μL McCoy's 5A medium containing 10%v/v FBS, 1% v/v penicillin/streptomycin and 1% v/v L-glutamine wereincubated in 96-well plates with compounds at various concentrations for72 h at 37° C. in a 5% CO₂ atmosphere. The compound dilutions were madein 100% DMSO followed by parallel dilutions in media. The finalconcentration of DMSO in each well was 0.05%. After 72 h, 20 μL of Celltiter 96 aqueous one solution (Promega Corporation, Madison, Wis.) wereadded to the cells and the plate was incubated at 37° C. for another 4h. The absorbance at 490 nm was then recorded on a 96-well plate reader(Spectramax M2, Molecular Devices, Sunnyvale, Calif.). Data analysis wasperformed in Microsoft Excel (Microsoft Corp, Redmond, Wash.).((O.D.sample−average O.D. positive control)/(average O.D. negativecontrol−average O.D. positive control))*100, where O.D. is the measuredabsorbance, O.D. positive control is the absorbance from cells incubatedwith trichostatin A at 5 μM and O.D. negative control is the absorbancemeasured from cells incubated without any compound, was plotted againstcompound concentration and an IC50 was determined by graphicalinterpolation of the concentration required for 50% inhibition of cellgrowth. IC50's are presented in Table 2, where A stands for IC50 lessthan 5 μM, B covers the range between 5 and 10 μM, C is from 10 to 20μM, and IA is used for IC50 greater than 20 μM.

Effect of HDAC Inhibitors on Frataxin (FXN) mRNA Expression

Blood is collected from Friedreich's ataxia patient donors into tubescontaining the anti-coagulant EDTA. Primary lymphocytes are isolatedusing Lymphocyte Separation Medium (MP Biomedicals, Solon, Ohio)following the manufacturer's instructions and including a fewmodifications made by Repligen. After a final wash in Phosphate BufferedSaline (PBS), the cells are distributed into a 6-well cell culture platein cell growth medium. The test HDAC inhibitor compound is added tocells in a dose escalating manner (usually concentrations range from 1to 10 μM) and 0.1% DMSO is added to one well of cells as a no treatmentcontrol. Cells are incubated for 48 hours at 37° C. in a CO₂ incubator;cell counts are taken using a Countess automated cell counter(Invitrogen, Carlsbad, Calif.). Equivalent numbers of cells for alltreatment conditions are pelleted by centrifugation and resuspended incell lysis buffer. Total RNA is isolated from approximately 1×10⁶primary lymphocytes using a RNeasy Mini Kit (Qiagen, Valencia, Calif.),following the manufacturer's instructions and including an optionalon-column DNAse digestion step. The isolation is performed eithermanually or using the QIAcube (Qiagen, Valencia, Calif.), an instrumentthat automates much of the isolation procedure. The RNA yield andconcentration is determined using a Nanodrop spectrophotometer (ThermoFisher Scientific, Waltham, Mass.) and depending on the RNAconcentration, one of two protocols is used to measure frataxin (FXN)transcript levels. For samples containing at least 15 ng/μL RNA aTaqMan® Probe-based (Applied Biosystems, Carlsbad, Calif.) qRT-PCRmethod is used, while for samples containing less than 15 ng/μL RNA aSYBR Green qRT-PCR method is used. In the TaqMan® Probe-based methodspecific primer/probe pairs for FXN and GAPDH are multiplexed in eachreaction. In the SYBR Green method FXN and GAPDH are amplified inseparate reactions. In both methods each RNA sample is analyzed intriplicate (preferably) or duplicate (minimally) using a one-stepqRT-PCR master mix that contains all the components necessary for cDNAsynthesis and PCR amplification in a single, continuous reaction. Aftercycling is complete, MxPro Software (Agilent Technologies, Santa Clara,Calif.) is used to analyze the collected data and determine the relativeamount of FXN mRNA compared to a control sample. An adaptive baselinemethod is used for baseline correction whereby an algorithmautomatically selects the appropriate baseline cycles for each well andeach dye. An amplification-based threshold is set and the correspondingthreshold cycle, or Ct, is obtained for calculating targetconcentration. The Ct values for each target gene (FXN and GAPDH) foreach replicate series are averaged. The amount of FXN (or GAPDH) in thesample is determined as the relative quantity to the calibrator wherethe calibrator sample is assigned an arbitrary quantity of 1. Thefollowing equation is used: Relative quantity to the calibrator=2^(−ΔCt)where ΔCt=(Ct_gene)unknown−(Ct_gene)calibrator, gene is either FXN orGAPDH, calibrator is a DMSO control sample, and unknown is a HDACitreated sample. The relative quantity of FXN is normalized to cellnumber and RNA input. Data is reported in Tables 2 and 4 below, wherethe concentration required for a 2-fold increase in FXN mRNA is reportedas A if less than 5 μM, B if between 5 and 10 μM, C if greater than 10μM.

TABLE 2 acid stability, cell deacetylase inhibition, anti-proliferation,frataxin mRNA expression and tissue distribution assay results compoundacid stability 850 DAC Hct-116 FXN 2x BPR F1 B IA IA F2 B D A A A F3 B BA A C F4 B B A A B A1 IA B A2 B D IA B A3 IA A5 B C D1 A B B A B D2 IAIA C C D3 A B A B C D10 C IA C B D4 A C IA C C D7 B C A B B D9 A B B A BD8 B A C C D5 C IA D D6 D IA C IA A6 IA C D E2 A D IA A A7 IA B A8 B D BA9 IA G1 B IA D14 B C B D11 B B A D12 A B B D13 B IA A10 D C A11 A A C1IA B E1 IA D15 B B1 D F5 C F6 D C3 IA B6 C B2 C B4 D C B3 B C D16 D G2 DIA B5 C C A12 IAProtocol for Compound Stability in Hepatocytes

To assess the stability and metabolism of RGFP compounds in hepatocytes.This assay was designed to evaluate the metabolism of RGFP compounds,following their incubation with human, monkey, dog and rat hepatocytesby monitoring either parent drug disappearance or metabolite appearanceusing HPLC. The results are shown in Table 4 ((% Left in Hep: IA<10%,50%<A, 50%>B>30%, 30%>C>10%, ND: not determined).

Equipment:

-   -   Applied Biosystem Triple Quadrupole LC/MS/MS    -   Ice bucker, timer    -   96 well plates; Falcon, Cat#353072    -   96 well plates shaker    -   Various pipettes: 10 μL, 20 μL, 200 μL, and 1000 μL    -   Test tubes: Catalog # VWR 47729-572, 13×100 mm

TABLE 3 Materials and Reagents Item Vendor Catalog # Human HepatocytesCelsis X008001 Monkey Hepatocytes Celsis M00350 Dog Hepatocytes CelsisM00205 Rat Hepatocytes Celsis M00005 Torpedo Antibiotix Mix InvitroTechnologies Z99000 In VitroGRO HT Medium Celsis Z99019 In VitroGRO KHBCelsis Z99074 Acetonitrile Fisher A-9981 Methanol Fisher A-4521 TrypanBlue Solution Sigma Chemical T-8154Procedure:

-   -   Turn on the water-bath heater to 37° C.    -   Take out the KHB buffer and make sure it is at room temp before        use    -   Prepare 2.5 mM concentration of RGFP compound in DMSO stock    -   Add 10 μL of above DMSO stock to 2490 μL KHB buffer; final        concentration of RGFP compound will be 10 μM    -   Pre-warm 45 ml InVitro HT Medium to 37° C. in a sterile 50 ml        conical tube    -   Add 1.0 mL Torpedo Antibiotic Mix per 45 mL InVitro HT medium    -   Transfer 13 mL of warm HT medium with Antibiotic Mix into a 15        mL conical tube.    -   Carefully remove the hepatocyte vials from liquid nitrogen        (liquid phase).    -   Immediately immerse the vial into a 37° C. water bath. Shake        gently until the ice melts entirely. Do not keep the cells in        37° C. water bath longer than necessary.    -   Immediately empty contents of the vial into 13 ml of pre-warmed        InVitro HT Medium with antibiotics. Rinse the vial with the HT        media that you have just transferred the hepatocytes to, in        order to ensure complete transfer    -   Centrifuge the cell suspension at 600 RPM for 5 minutes at room        temperature.    -   Discard the supernatant by either pouring in one motion (do not        pour partially and re-invert centrifuge tube) or aspirating        using a vacuum pump    -   Add 1.0 ml of KHB (at room temperature) buffer to the tube of        hepatocyte pellet. Loosen the cell pellet by gently swirling the        centrifuge tube    -   Transfer 100 μL of above solution to a different tube and add        900 μL of KHB buffer to count the cells    -   Determine the total cell count and the number of viable cells        using the Trypan Blue exclusion method    -   Once you obtain the cell count, multiply the number by 10        (attributing to the dilution factor)    -   Now add required volume of KHB buffer to the tube containing        hepatocytes such that the final count will be 2 million cells/mL    -   Dispense 50 μL of 2 million cells/ml to a 96 well plate and then        add 50 μl of DMSO stock to respective wells (such that, the        concentration of RGFP compounds is 5 μM and number of cells are        100000 in each well)    -   Place the plates on a shaker in a 37° C. incubator with 5% CO₂    -   Separate plates for each time point are advisable (Time points:        0 h, 1 h, 2 h, and 6 h)    -   After each time point, add 100 μL of quenching solution.    -   Quenching solution is an acetonitrile solution containing        RGFP531 (10 μM) internal standard, 0.1% formic acid and        phenylglyoxol (400 μM). The formic acid and phenylglyoxal is        used for the identification and quantification of OPD as        mentioned above.    -   Pipette up and down a few times to ensure a complete stop of        reaction    -   Transfer all the solution into a 1.5 ml tube, vortex thoroughly,        and centrifuge at 14000 RPM at 4° C. for 5 minutes to        precipitate cell debris

Transfer the 150 μL of supernatant to vials for analysis using HPLC

TABLE 4 HDAC1 HDAC2 HDAC3 Coding Structure MW clogP tPSA IC50 (uM) IC50(uM) IC50 (uM) F7 

IA 3.50 71   A A A F8 

A 3.52 58   A A A F9 

B 1.09 64   A ND A F10

A 3.29 58   A ND A F11

A 2.07 64   A B A F12

A 2.38 58   A A A F13

A 3.10 58   A A A F14

A 4.15 58   A A A F15

A 2.43 79   A A A F16

A 2.37 70.7 A A A F17

A 3.37 58.4 A A A F18

A 1.87 70.7 A A A F19

A 1.71 78.6 A B A F20

A 2.88 58.3 B B A Cmax brain DAC IC50 F × n > 2X % left Coding BPR(ng/m) (uM) (uM) 6 h Hum F7  ND ND C ND C F8  C C A ND A F9  ND ND A NDIA F10 A A C ND B F11 A A A ND C F12 A A A A A F13 A A ND ND B F14 A A BA C F15 A A B A A F16 ND ND ND ND C F17 ND ND ND ND C F18 ND ND ND ND CF19 ND ND ND ND A F20 ND ND ND ND AEffect of Compounds on Long Term Memory for Object Recognition

C57BL/6J male mice were handled 1-2 min for 5 days and were habituatedto the experimental apparatus 5 min a day for 4 consecutive days in theabsence of objects. During the training trial, mice were placed in theexperimental apparatus with two identical objects and were allowed toexplore these objects for 3 min, which does not result in short- orlong-term memory (Stefanko et al., 2009). Immediately followingtraining, mice received subcutaneous injections of either vehicle (20%glycerol, 20% PEG 400, 20% propylene glycol, and 100 mM sodium acetate,pH 5.4), reference compound 1, RGFP109, class I HDAC inhibitor, (3, 10,30 mg/kg), reference compound 2, RGFP136 (3, 10, 30 mg/kg), or compoundD2 (3, 10, 30 mg/kg). 24-h later mice were tested for memory retention(5 min) using the object recognition memory task (ORM), in which afamiliar object was replaced with a novel one. All training and testingtrials were videotaped and analyzed by individuals blind to thetreatment condition and the genotype of subjects. A mouse was scored asexploring an object when its head was oriented toward the object withina distance of 1 cm or when the nose was touching the object. Therelative exploration time was recorded and expressed by a discriminationindex [DI=(tnovel−tfamiliar)/(tnovel+tfamiliar)×100].

All doses of the compounds significantly enhanced long-term memoryformation compared to vehicle-treated mice (FIGURE). Dose dependenteffects were seen with RGFP 109 and 136, but there was no effect of dosefor D2. The lack of an observed dose effect for D2 is likely due to itsenhanced brain penetration, such that 3 mg/kg is sufficient to producethe full behavioral effect. See FIGURE.

Other Embodiments

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

We claim:
 1. A method of inhibiting HDAC1, HDAC2, or HDAC3 in a subject,comprising administering to the subject an effective amount of acompound having a structure of formula (II):

wherein: R^(A) is H or F; R^(C) is H, Cl, or F; Het is selected fromoxetanyl, azetindinyl, piperidinyl, and 8-azabicyclo[3.2.1]octanyl, andwhen Het is azetindinyl, piperidinyl, or 8-azabicyclo[3.2.1]octanyl, thering nitrogen is substituted with R^(B); and R^(B) is C₁-C₆alkyl,C₁-C₆hydroxyalkyl, C₁-C₃alkylene-C₃-C₆cycloalkyl, C₁-C₃alkylene-phenyl,or C₁-C₃alkylene-pyridyl; wherein the phenyl or pyridyl ring isoptionally substituted with methyl; or a pharmaceutically acceptablesalt thereof.
 2. The method of claim 1, wherein R^(A) is H.
 3. Themethod of claim 1, wherein R^(A) is F.
 4. The method of claim 1, whereinHet is oxetanyl.
 5. The method of claim 1, wherein Het is azetindinyl,piperidinyl, or 8-azabicyclo [3.2.1]octanyl.
 6. The method of claim 1,wherein Het is azetindinyl or piperidinyl.
 7. The method of claim 1,wherein R^(B) is C₁₋₆alkyl, C₁₋₆hydroxyalkyl, CH₂-cyclopropyl,CH₂-phenyl, or CH₂-pyridyl, and the pyridyl is optionally substitutedwith methyl.
 8. The method of claim 1, wherein R^(B) is methyl,CH₂C(CH₃)₃, CH₂C(CH₃)₂OH, CH₂-cyclopropyl, CH₂-phenyl, CH₂-pyridyl, orCH₂-methylpyridyl.
 9. The method of claim 1, wherein Het is azetindinyl,piperidinyl, or 8-azabicyclo [3.2.1]octanyl; and R^(B) is C₁₋₆alkyl,C₁₋₆hydroxyalkyl, CH₂-cyclopropyl, CH₂-phenyl, or CH₂-pyridyl, orCH₂-methylpyridyl.
 10. The method of claim 9, wherein Het isazetindinyl, and R^(B) is C₁₋₆alkyl, CH₂C(CH₃)₂OH, CH₂-cyclopropyl,CH₂-phenyl, or CH₂-methylpyridyl.
 11. The method of claim 9, wherein Hetis piperidinyl, and R^(B) is C₁₋₆alkyl, CH₂C(CH₃)₂OH, CH₂-cyclopropyl,CH₂-phenyl, CH₂-pyridyl, or CH₂-methylpyridyl.
 12. The method of claim9, wherein Het is 8-azabicyclo [3.2.1]octanyl and R^(B) is C₁₋₆alkyl.13. The method of claim 1, wherein the subject suffers from aneurological disease.
 14. The method of claim 13, wherein theneurological disease is Friedreich's ataxia.
 15. A method of treating aneurological disease or disorder selected from Friedreich's ataxia,myotonic dystrophy, spinal muscular atrophy, fragile X syndrome,Huntington's disease, spinocerebellar ataxia, Kennedy's disease,amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, andAlzheimer's disease; cutaneous T-cell lymphoma; a B cell lymphoma;colorectal cancer; psoriasis; rheumatoid arthritis; osteoarthritis; along-term memory impairment condition; or a drug addiction in a subjectin need thereof, the method comprising administering to the subject aneffective amount of a compound having a structure of formula (II):

wherein: R^(A) is H or F; R^(C) is H, Cl, or F; Het is selected fromoxetanyl, azetindinyl, piperidinyl, and 8-azabicyclo[3.2.1]octanyl, andwhen Het is azetindinyl, piperidinyl, or 8-azabicyclo[3.2.1]octanyl, thering nitrogen is substituted with R^(B); R^(B) is C₁-C₆alkyl,C₁-C₆hydroxyalkyl, C₁-C₃alkylene-C₃-C₆cycloalkyl, C₁-C₃alkylene-phenyl,or C₁-C₃alkylene-pyridyl; wherein the phenyl or pyridyl ring isoptionally substituted with methyl; or a pharmaceutically acceptablesalt thereof.
 16. The method of claim 15, wherein Het is azetindinyl,piperidinyl, or 8-azabicyclo [3.2.1]octanyl.
 17. The method of claim 15,wherein Het is azetindinyl or piperidinyl.
 18. The method of claim 15,wherein R^(B) is C₁₋₆alkyl, C₁₋₆hydroxyalkyl, CH₂-cyclopropyl,CH₂-phenyl, or CH₂-pyridyl, wherein the pyridyl is optionallysubstituted with methyl.
 19. The method of claim 15, wherein Het isazetindinyl, piperidinyl, or 8-azabicyclo [3.2.1]octanyl; and R^(B) isC₁₋₆alkyl, CH₂C(CH₃)₂OH, CH₂-cyclopropyl, CH₂-phenyl, or CH₂-pyridyl,wherein the pyridyl is optionally substituted with methyl.
 20. A methodof treating a neurological disease or disorder selected fromFriedreich's ataxia, myotonic dystrophy, spinal muscular atrophy,fragile X syndrome, Huntington's disease, spinocerebellar ataxia,Kennedy's disease, amyotrophic lateral sclerosis, spinal and bulbarmuscular atrophy, and Alzheimer's disease; cutaneous T-cell lymphoma; aB cell lymphoma; colorectal cancer; psoriasis; rheumatoid arthritis;osteoarthritis; a long-term memory impairment condition; or a drugaddiction in a subject in need thereof, the method comprisingadministering to the subject an effective amount of a compound selectedfrom the group consisting of:

or a pharmaceutically acceptable salt thereof.
 21. The method of claim20, wherein the disease or disorder is Friedreich's ataxia.
 22. A methodof inhibiting HDAC1, HDAC2, or HDAC3 in a subject, the method comprisingadministering to the subject an effective amount of a compound selectedfrom the group consisting of:

or a pharmaceutically acceptable salt thereof.
 23. The method of claim22, wherein the subject suffers from a neurological disease.
 24. Themethod of claim 23, wherein the neurological disease is Friedreich'sataxia.